gmane.science.biology.informatics.conductor http://blog.gmane.org/gmane.science.biology.informatics.conductor hourly 1 1901-01-01T00:00+00:00 Gmane http://gmane.org/img/gmane-25t.png http://gmane.org summarizeOverlaps: ambiguous method dispatch http://comments.gmane.org/gmane.science.biology.informatics.conductor/48231 <pre>Entering this code: library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(LungCancerLines) exons &lt;- exons(TxDb.Hsapiens.UCSC.hg19.knownGene, vals = list(gene_id = "7157")) counts &lt;- summarizeOverlaps(exons, LungCancerBamFiles()) Yields: Note: method with signature 'GAlignments#Vector' chosen for function 'countOverlaps', target signature 'GAlignments#GRanges'. "Vector#GenomicRanges" would also be valid Note: method with signature 'GAlignments#Vector' chosen for function 'countOverlaps', target signature 'GAlignments#GRanges'. "Vector#GenomicRanges" would also be valid While this is apparently harmless, a couple of questions: - What is the rationale for defining countOverlaps methods on 'Vector'? If this is a simple wrapper, why not go all the way to ANY? - Would it be feasible to avoid these Notes (which probably unnecessarily worry the user), for example by defining specific methods for GenomicRanges and GRangesList? I realize that dual dispatch is inherently prone to ambiguities, but some brute-forcing might be worth the effort. Michael [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Michael Lawrence 2013-05-18T23:38:48 Annotation of Human Exon 1.0 ST http://comments.gmane.org/gmane.science.biology.informatics.conductor/48230 <pre> Hi list, I am having trouble trying to annotate a Human Exon 1.0 ST expression set. I know little about R and bioconductor and I find it hard to understand the instructions I find on the web. When analyzing HGU 133 Plus 2.0 arrays, I just had to follow these instructions: library("hgu133plus2.db") symbol &lt;- hgu133plus2SYMBOL genename &lt;- hgu133plus2GENENAME symbols &lt;- unlist(as.list(hgu133plus2SYMBOL)) genenames &lt;- unlist(as.list(hgu133plus2GENENAME)) results &lt;- cbind(symbols,genenames,exprs.eset) And the “results” would be the expression matrix with genenames and genesymbols associated to each affymetrix gene ID. I am trying to get the same results (the same matrix) for the Human Exon chip. I have summarized my data to the gene level using the oligo package and created the expression matrix: geneSummaries &lt;- rma(abatch.raw, target="core") expressionMatrix &lt;- exprs (geneSummaries) Now I understand that the best option is to use the biomaRt package to annotate, I have been reading the vignette but I am completely lost as for what I should do to just attach genenames, symbols, or some other identifier to the expression matrix. Could somebody tell me which commands or which steps I should follow? Thank you very much -- output of sessionInfo(): no sessioninfo -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Laura [guest] 2013-05-18T18:56:48 R crash on getBM query http://comments.gmane.org/gmane.science.biology.informatics.conductor/48218 <pre>Good afternoon, I am contacting you for an information regarding biomaRt, I have already contacted the BioMart helpdesk but they suggested to email you, as this is probably a bug of the biomaRt package. Every time I try to get annotation info on a SNP using biomaRt, the R console crashes. The session info are: R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base And the commands that I use are: library(biomaRt) snp.db = useMart("ENSEMBL_MART_SNP",host="www.ensembl.org&lt;http://www.ensembl.org&gt;",dataset="hsapiens_snp") variant = list(9,133271654) var_info = getBM(c("chr_name","chrom_start","allele","minor_allele","minor_allele_freq"),c("chr_name","chrom_start"),variant,snp.db) R always crashes at this point, also on other computers. I am using R 3.0.1 and the biomaRt package is up to date. Where could the problem be? Thanks a lot for the assistance! Francesco Mazzarotto [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Mazzarotto, Francesco 2013-05-17T15:27:24 Reminder: Course: Intermediate R / Bioconductor for High-Throughput Sequence Analysis, 28-29 May, Seattle http://comments.gmane.org/gmane.science.biology.informatics.conductor/48209 <pre>Bioconductors! There are still spaces in our forthcoming intermediate course on use of R / Bioconductor for high-throughput sequence analysis, a brief outline of which is below. More Information: https://secure.bioconductor.org/Seattle-May-2013/ Intermediate R / Bioconductor for High-Throughput Sequence Analysis introduces users with some R experience to common Bioconductor work flows for sequence analysis. The course involves a combination of presentations and hands-on exercises. Our starting point is BAM files created by aligning short reads to a reference genome. Topics include: exploratory analysis (GenomicRanges, Rsamtools); assessing differential expression of known genes (DESeq); detection, calling, and manipulation of variants (VariantTools, VariantAnnotation). We learn how to integrate results with curated gene and genomic annotations (GenomicFeatures), and to visualize results (GViz, ggbio). See you in Seattle, Martin </pre> Martin Morgan 2013-05-17T16:48:04 ShortRead 3' trimming negative length vectors are not allowed http://comments.gmane.org/gmane.science.biology.informatics.conductor/48208 <pre>Hello everyone, I am trying to do some quality trimming on some RNA seq reads (Illumina, 100 bp, single end). I have been following the pipeline from the UCR manuals&lt;http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Trimming-Low-Quality-3-Tails-from-R&gt; but I have run into an error I can't seem to resolve. library(ShortRead) reads &lt;- readFastq("myFile.fastq") qualityCutoff &lt;- 10 # remove read tails with quality lower than this seqs &lt;- sread(reads) # get sequence list qual &lt;- PhredQuality(quality(quality(reads))) # get quality score list as PhredQuality [1] 39145018 nrow=length(qual), byrow=TRUE) Error in .Call(.NAME, ..., PACKAGE = PACKAGE) : negative length vectors are not allowed as(qual, matrix) gives the same error, and as.matrix(qual) does as well, not sure how those two commands are different, but tried anyway. If I run the exact same commands, instead of the full 39145018 reads, I use the first 100, it works like a charm. I am working on a linux cluster, if that is important Does anyone have an idea? Cheers! </pre> Sam McInturf 2013-05-17T16:19:48 Genentech Bioinformatics is seeking R programming contractors http://comments.gmane.org/gmane.science.biology.informatics.conductor/48201 <pre>Dear all, The Genentech Bioinformatics department relies heavily on R for working with data. We need some assistance tightening up our low-level R-based infrastructure for processing sequencing and expression data. If you're a skilled R programmer (i.e., comfortable with S4, etc), like big data, and have some cycles to spare for contracting work, please send me an email with your CV. We strongly prefer on-site work, so preference is given to local (Bay Area) contractors. Thanks, Michael [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Michael Lawrence 2013-05-17T12:06:47 Bioconductor error http://comments.gmane.org/gmane.science.biology.informatics.conductor/48200 <pre>Dear all, I am getting a strange error this morning from Bioconductor. I am trying to connect from different servers and I'm still getting the same error. Are there some database connection problems from Bioconductor? Error: Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "ensembl_exon : Query ERROR: caught BioMart::Exception::Database: Could not connect to matabase ensembl_mart_69: DBI connect('database=ensembl_mart_69;host=bm_myst=3306','bmweb',...) failed: Host '54.225.80.241' is blocked because of manection errors; unblock with 'mysqladmin flush-hosts' at /srv/ biomart_servmart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 Code example: #load Bioconductor source("http://bioconductor.org/biocLite.R") #load package GenomeGraphs library(GenomeGraphs) mart &lt;- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") makeGeneRegion(start=105800000, end=107800000, strand="+", chromosome="7", biomart=mart) Thanks [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Alexia Cardona 2013-05-17T11:48:37 topGO desperation http://comments.gmane.org/gmane.science.biology.informatics.conductor/48198 <pre>Hey Jim, well I guess the problem lies somewhere in how the file is built up. But I cannot find how it should be. setwd("/Users/christianoertlin/Desktop/Stage files/R") read.csv("first.csv", header=TRUE, sep=",") library(topGO) read.table("first.csv",header=TRUE,sep=",") resultFisher &lt;- runTest("first.csv", algrotithm="classic",statistic="Fisher") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘runTest’ for signature ‘"character", "missing", "character"’ This is my problem. The fisher test does not recognize my file as something to work with. I tried moving some rows in the file but it did not work either. Tbh I have no clue what is wrong with it. I added the file in the mail. The file is an output generated by GO-elite. I already have my GO term with an outcome I just want to do some test and map them into a graph. Like it is done with the from the topGO example. showSigOfNodes(GOdata, score(resultKS.elim), firstSigNodes = 5, useInfo = 'all') Kind Regards, Christian _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor</pre> Oertlin, Christian (Stud. FHML 2013-05-16T12:14:14 analyze three factors in Limma http://comments.gmane.org/gmane.science.biology.informatics.conductor/48197 <pre>Hi! I would in a microarray experiment analyze three factors simultaneously in Limma, treatment, group (i.e. gender), and study center. Is it possible to include three factors simultaneously in an interaction model? Can I use the “sum to zero” parameterization as described in Section 8.5.4 of the user guide? Any more specific recommendation on how to proceed? /Ingrid [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor</pre> Ingrid Dahlman 2013-05-16T19:57:37 Working with non-type strain annotation http://comments.gmane.org/gmane.science.biology.informatics.conductor/48196 <pre>Hi I'm doing proteomics on industrial bacterial strains. The genomes of these strains are almost completed (no joining of contigs) and my main genomic data is thus a list of CDS's. I have functionally annotated these using Blast2Go, and have thus GO terms, possibly EC number and Uniprot ID for the closest match for most of the CDS's. My question is thus: How do I best proceed with this data in the Bioconductor framework, when I want to do things suchs as gene set enrichment analysis etc. Is the best approach to build my own Annotation packages for each strain or is there a simpler 'ad hoc' data structure that supports the same functionality? It seems that most of the tutorials etc. supposes that you work on type strains (which is also probably true for the most part) where an annotation package is readily available… best Thomas _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Thomas Dybdal Pedersen 2013-05-16T08:30:28 looking for tools to study additive expression effects ingene pathways/networks http://comments.gmane.org/gmane.science.biology.informatics.conductor/48194 <pre>Hi, We are seeking recommendations for approaches to study how gene expression effects may become additive within pathways. We have logFC values for genes differentially expressed in a comparison of control to treatment. We are interested in the following problem: Genes A and B exhibit a modest increase in expression of 1.5 fold each and exist in the pathway A-&gt;B-&gt;C. Therefore, we expect the effects of the expression changes for A and B to become additive, yielding a net effect on C that is increased by 3-fold compared to baseline. We wish to identify, visualize and study these scenarios within KEGG annotated pathways. I expect that this sort of analysis is implemented in software intended to study complex networks, but can't see it obviously available in Rgraphviz or KeggGraph, for example. Expert advice would be greatly appreciated. Thank you. best wishes, Chris Christopher Gregg, PhD. New York Stem Cell Foundation-Robertson Investigator Assistant Professor, Neurobiology and Anatomy Adjunct Assistant Professor, Human Genetics 323 Wintrobe Bldg 530 University of Utah, School of Medicine 20 North 1900 East Salt Lake City, Utah 84132-3401 phone: (801) 581-8212 fax: (801) 585-9736 ------------------------------------ Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> chris_utah 2013-05-16T22:59:58 how to deal with antisense gene in DESeq or edgeR? http://comments.gmane.org/gmane.science.biology.informatics.conductor/48193 <pre>now i have strand specific data, usually i only keep the sense strand data for DE analysis？ but I found many antisense genes? do i need combine them ? for exaple: gene1 value1 value2 gene2 value1 value2 ... gene1-antisense value1 value2 </pre> Wang Peter 2013-05-16T21:16:42 Creating an OrganismDbi package with a few transcriptannotations http://comments.gmane.org/gmane.science.biology.informatics.conductor/48192 <pre>Hi, I'd like to create an OrganismDbi package so that I can put extra annotations on the transcripts/genes in a TxDb package. My understanding is that I need a separate database package that I can join with the TxDb package. Do I need to make an OrgDb package? I looked into this a bit and it seems that there is little support for making a non-NCBI-based org package. Maybe I could create a new type of package with a simple table with a row for each transcript, including the gene symbol and whether the transcript is "canonical" according to UCSC. It looks like this process is documented here: http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/NewSchema.pdf. It also seems really involved. What's the path of least resistance here? Thanks, Michael [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Michael Lawrence 2013-05-16T20:50:55 QuasR: how to use an indexed reference genome? http://comments.gmane.org/gmane.science.biology.informatics.conductor/48191 <pre>I am new to QuasR, and alos quite new to aligning short reads to reference genomes more generally. I cannot figure out how to use a pre-built indexed reference genome file with QuasR. The examples supplied with the package work nicely. Scaling up to using all of hg19 raises problems for me. I apologize if I am missing the obvious. To illustrate the problem, I call QuasR's qAlign method with just two arguments (quoting from the man page): sampleFile: a text file listing input sequence files and sample names genome: the reference genome for primary alignments, one of: * a string referring to a "BSgenome" package (e.g. ""BSgenome.Hsapiens.UCSC.hg19""), which will be downloaded automatically from Bioconductor if not present * the name of a fasta sequence file containing one or several sequences (chromosomes) to be used as a reference QuasR apparently invokes the bowtie indexing program when supplied either of the two "genome" options: a BSgenome package, or a fasta file. But since indexing takes a long time -- hours, apparently -- I hoped to provide a ready-made index file, and found some described here: http://bowtie-bio.sourceforge.net/tutorial.shtml specifically ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip Various attempts to specify this file, or any of its contents (unzipped) to QuasR fail with these messages: Error: The specified genome /Users/pshannon/s/data/public/bowtie/indexes/hg19.1.ebwt does not have the extension of a fasta file (fa,fasta,fna)&gt; Error: The specified genome has to be a file and not a directory: /Users/pshannon/s/data/public/bowtie/indexes I'll be grateful for advice on how to do this properly. Thanks, - Paul R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.13.14 BSgenome_1.29.0 Biostrings_2.29.2 QuasR_1.1.4 GenomicRanges_1.13.12 XVector_0.1.0 [7] IRanges_1.19.8 BiocGenerics_0.7.2 Rbowtie_1.1.3 BiocInstaller_1.11.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.23.11 Biobase_2.21.2 DBI_0.2-7 GenomicFeatures_1.13.8 RCurl_1.95-4.1 [6] RSQLite_0.11.3 ShortRead_1.19.3 XML_3.95-0.2 biomaRt_2.17.0 bitops_1.0-5 [11] compiler_3.0.0 grid_3.0.0 hwriter_1.3 lattice_0.20-15 rtracklayer_1.21.5 [16] stats4_3.0.0 tools_3.0.0 zlibbioc_1.7.0 _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Paul Shannon 2013-05-16T20:48:47 problem with aveLogCPM.default in edgeR http://comments.gmane.org/gmane.science.biology.informatics.conductor/48190 <pre>Hi, I recently upgraded edgeR from 3.0.8 to 3.2.3 and I'm noticing some differences. I have some data that I normalized with EDASeq. I attempted to calculate the trended dispersion and I get the following error: Error in t(y) + prior.count.scaled : non-conformable arrays [1] "SeqExpressionSet" attr(,"package") [1] "EDASeq" [1] 19062 36 [1] 19062 36 The error seems to occur in the aveLogCPM.default function due to matrix addition on two matrices with differing dimensions. Line 34 reads as: abundance &lt;- mglmOneGroup(t(t(y)+prior.count.scaled),dispersion=dispersion,offset=offset) I no longer get an error if I change it to: abundance &lt;- mglmOneGroup(y+prior.count.scaled,dispersion=dispersion,offset=offset) I don't think this is the best solution to fix all scenarios since I don't know this code very well. So, I see some things have changed and I'm wondering if I need to make some changes in how I call the function or if there is really a bug of some kind here. Thanks in advance for your help, Suzy R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] EDASeq_1.6.0 aroma.light_1.30.1 matrixStats_0.8.1 ShortRead_1.18.0 [5] latticeExtra_0.6-24 RColorBrewer_1.0-5 Rsamtools_1.12.3 lattice_0.20-15 [9] Biostrings_2.28.0 GenomicRanges_1.12.3 IRanges_1.18.1 Biobase_2.20.0 [13] BiocGenerics_0.6.0 edgeR_3.2.3 limma_3.16.3 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.5 bitops_1.0-5 DBI_0.2-7 [5] DESeq_1.12.0 genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.0 [9] hwriter_1.3 R.methodsS3_1.4.2 RSQLite_0.11.3 splines_3.0.0 [13] stats4_3.0.0 survival_2.37-4 tools_3.0.0 XML_3.96-1.1 [17] xtable_1.7-1 zlibbioc_1.6.0 _________________________________ Suzy Stiegelmeyer, PhD Computational Biologist Bioinformatics Syngenta Biotechnology, Inc. 3054 Cornwallis Rd Research Triangle Park, NC 27709 USA phone +1 919 281 7472 suzy.stiegelmeyer-Lr/lmMrs2ylWk0Htik3J/w&lt; at &gt;public.gmane.org&lt;mailto:suzy.stiegelmeyer-Lr/lmMrs2ylWk0Htik3J/w&lt; at &gt;public.gmane.org&gt; www.syngenta.com&lt;http://www.syngenta.com/&gt; This message may contain confidential information. If yo...{{dropped:7}} _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> suzy.stiegelmeyer-Lr/lmMrs2ylWk0Htik3J/w< at >public.gmane.org 2013-05-16T19:57:53 library(\"geneplotter\") fails on load http://comments.gmane.org/gmane.science.biology.informatics.conductor/48187 <pre> Hello, I know the R code/version I am inquiring about is outdated, unfortunately I am trying to pick up the development thread pieces from someone who passed away several years ago. There are other components of the system integrated into the entire (extremely large and complex) system which disallow upgrading to a current kernel/system. It would require an impossible effort/cost. I am just learning how to work in this environment. I have no option but to make this work. The distribution in use: root&lt; at &gt;cit-calibration: # lsb_release -a No LSB modules are available. Distributor ID:Ubuntu Description:Ubuntu 8.10 Release:8.10 Codename:intrepid The error: root&lt; at &gt;cit-calibration:# R --vanilla R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: annotate Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'geneplotter' methods specified for export, but none defined: Makesense, imageMap In addition: Warning messages: 1: '.__M__Makesense:geneplotter' looks like a pre-2.4.0 S4 object: please recreate it 2: '.__M__imageMap:geneplotter' looks like a pre-2.4.0 S4 object: please recreate it 3: 'Makesense' looks like a pre-2.4.0 S4 object: please recreate it 4: 'imageMap' looks like a pre-2.4.0 S4 object: please recreate it Error: package/namespace load failed for 'geneplotter' I would re-create them, if I could determine how to do it. I have downloaded the R source and recompiled from scratch. As can be seen from the listing below, the geneplotter directory has not been touched (along with some others). I do not know why. root&lt; at &gt;cit-calibration: # ls -ltr /usr/local/lib/R/site-library drwxr-sr-x 10 root staff 4096 Sep 8 2005 sma drwxr-sr-x 11 root staff 4096 Sep 8 2005 sfsmisc drwxr-sr-x 11 root staff 4096 Sep 8 2005 waveslim drwxr-sr-x 10 root staff 4096 Sep 8 2005 pls.pcr drwxr-sr-x 12 root staff 4096 Feb 9 2006 vegan drwxr-sr-x 12 root staff 4096 Feb 9 2006 ade4 drwxr-sr-x 11 root staff 4096 Feb 10 2006 mvpart drwxr-sr-x 14 root staff 4096 Nov 28 2006 reposTools drwxr-sr-x 10 root staff 4096 Nov 28 2006 xtable drwxr-sr-x 11 root staff 4096 Nov 28 2006 annaffy drwxr-sr-x 11 root staff 4096 Nov 28 2006 annotate drwxr-sr-x 13 root staff 4096 Nov 28 2006 genefilter drwxr-sr-x 11 root staff 4096 Nov 28 2006 geneplotter drwxr-sr-x 17 root staff 4096 May 15 11:51 Biobase drwxr-sr-x 15 root staff 4096 May 15 11:51 Biostrings drwxr-sr-x 9 root staff 4096 May 15 11:51 DynDoc drwxr-sr-x 10 root staff 4096 May 15 11:51 GO drwxr-sr-x 10 root staff 4096 May 15 11:51 KEGG drwxr-sr-x 11 root staff 4096 May 15 11:51 KernSmooth drwxr-sr-x 11 root staff 4096 May 15 11:52 MNP drwxr-sr-x 12 root staff 4096 May 15 11:52 MatchIt drwxr-sr-x 9 root staff 4096 May 15 11:52 RColorBrewer drwxr-sr-x 11 root staff 4096 May 15 11:52 ROC drwxr-sr-x 13 root staff 4096 May 15 11:52 RUnit drwxr-sr-x 10 root staff 4096 May 15 11:52 Rserve drwxr-sr-x 9 root staff 4096 May 15 11:52 abind drwxr-sr-x 10 root staff 4096 May 15 11:52 acepack drwxr-sr-x 10 root staff 4096 May 15 11:52 affyio drwxr-sr-x 10 root staff 4096 May 15 11:52 cclust drwxr-sr-x 9 root staff 4096 May 15 11:52 codetools drwxr-sr-x 10 root staff 4096 May 15 11:52 date drwxr-sr-x 11 root staff 4096 May 15 11:52 eco drwxr-sr-x 10 root staff 4096 May 15 11:52 getopt drwxr-sr-x 9 root staff 4096 May 15 11:52 gmodels drwxr-sr-x 11 root staff 4096 May 15 11:52 gtools drwxr-sr-x 10 root staff 4096 May 15 11:52 hgu95av2 drwxr-sr-x 10 root staff 4096 May 15 11:52 limma drwxr-sr-x 10 root staff 4096 May 15 11:53 lpSolve drwxr-sr-x 10 root staff 4096 May 15 11:53 mapproj drwxr-sr-x 11 root staff 4096 May 15 11:53 misc3d drwxr-sr-x 10 root staff 4096 May 15 11:53 mnormt drwxr-sr-x 11 root staff 4096 May 15 11:53 mvtnorm drwxr-sr-x 13 root staff 4096 May 15 11:53 nws drwxr-sr-x 12 root staff 4096 May 15 11:53 permute drwxr-sr-x 10 root staff 4096 May 15 11:53 polspline drwxr-sr-x 11 root staff 4096 May 15 11:53 preprocessCore drwxr-sr-x 10 root staff 4096 May 15 11:53 psy drwxr-sr-x 9 root staff 4096 May 15 11:53 relimp drwxr-sr-x 11 root staff 4096 May 15 11:53 sandwich drwxr-sr-x 13 root staff 4096 May 15 11:53 urca drwxr-sr-x 13 root staff 4096 May 15 11:54 affy drwxr-sr-x 9 root staff 4096 May 15 11:54 fBonds drwxr-sr-x 10 root staff 4096 May 15 11:54 gregmisc drwxr-sr-x 12 root staff 4096 May 15 11:54 its drwxr-sr-x 12 root staff 4096 May 15 11:54 marray drwxr-sr-x 13 root staff 4096 May 15 11:54 multtest drwxr-sr-x 10 root staff 4096 May 15 11:55 GO.db drwxr-sr-x 10 root staff 4096 May 15 11:55 KEGG.db drwxr-sr-x 12 root staff 4096 May 15 11:55 affydata drwxr-sr-x 10 root staff 4096 May 15 11:55 hgu95av2.db drwxr-sr-x 15 root staff 4096 May 15 11:55 matchprobes drwxr-sr-x 13 root staff 4096 May 15 11:55 vsn drwxr-sr-x 12 root staff 4096 May 15 11:55 gcrma drwxr-sr-x 11 root staff 4096 May 15 11:55 affyPLM drwxr-sr-x 12 root staff 4096 May 15 11:55 affyQCReport -rw-r--r-- 1 root staff 866 May 15 11:55 R.css Library environment variable: root&lt; at &gt;cit-calibration: echo $R_LIBS_SITE /usr/local/lib/R/site-library [1] ".GlobalEnv" "/usr/lib64/R/library/stats" [3] "/usr/lib64/R/library/graphics" "/usr/lib64/R/library/grDevices" [5] "/usr/lib64/R/library/utils" "/usr/lib64/R/library/datasets" [7] "/usr/lib64/R/library/methods" "Autoloads" [9] "/usr/lib64/R/library/base" I have tried this sequence: which of course downloads and rebuilds all the packages. There were 29 warnings from this procedure. Running biocinstall version 2.2.11 with R version 2.7.1 Your version of R requires version 2.2 of BioConductor. Originally I had 29 warnings (several re-attempts): 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : packages ~&lt; at &gt;~Xade4~&lt; at &gt;~Y, ~&lt; at &gt;~Xmvpart~&lt; at &gt;~Y, ~&lt; at &gt;~Xpls.pcr~&lt; at &gt;~Y, ~&lt; at &gt;~XreposTools~&lt; at &gt;~Y, ~&lt; at &gt;~Xsfsmisc~&lt; at &gt;~Y, ~&lt; at &gt;~Xsma~&lt; at &gt;~Y, ~&lt; at &gt;~Xwaveslim~&lt; at &gt;~Y, ~&lt; at &gt;~Xxtable 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : dependencies ~&lt; at &gt;~XtimeDate~&lt; at &gt;~Y, ~&lt; at &gt;~XtimeSeries~&lt; at &gt;~Y, ~&lt; at &gt;~Xstabledist~&lt; at &gt;~Y, ~&lt; at &gt;~Xgss~&lt; at &gt;~Y, ~&lt; at &gt;~XRSQLite~&lt; at &gt;~Y are not available 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fBasics' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'Hmisc' had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'RGtk2' had non-zero exit status 6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'rsprng' had non-zero exit status 7: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'XML' had non-zero exit status 8: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'AnnotationDbi' had non-zero exit status 9: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'vegan' had non-zero exit status 10: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fArma' had non-zero exit status 11: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fNonlinear' had non-zero exit status 12: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fOptions' had non-zero exit status 13: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fTrading' had non-zero exit status 14: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fUnitRoots' had non-zero exit status 15: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'multcomp' had non-zero exit status 16: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'rggobi' had non-zero exit status 17: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'sn' had non-zero exit status 18: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'annotate' had non-zero exit status 19: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fAsianOptions' had non-zero exit status 20: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fCopulae' had non-zero exit status 21: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fExoticOptions' had non-zero exit status 22: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fExtremes' had non-zero exit status 23: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fMultivar' had non-zero exit status 24: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'annaffy' had non-zero exit status 25: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'genefilter' had non-zero exit status 26: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'geneplotter' had non-zero exit status 27: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fAssets' had non-zero exit status 28: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fRegression' had non-zero exit status 29: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'simpleaffy' had non-zero exit status Today I get only 15: The downloaded packages are in /tmp/RtmpBQQJea/downloaded_packages There were 15 warnings (use warnings() to see them) Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : packages 'ade4', 'mvpart', 'pls.pcr', 'reposTools', 'sfsmisc', 'sma', 'waveslim', 'xtable', 'VR', 'base', 'boot', 'cluster', 'datasets', 'foreign', 'grDevices', 'graphics', 'grid', 'lattice', 'methods', 'mgcv', 'nlme', 'rpart', 'splines', 'stats', 'stats4', 'survival', 'tcltk', 'tools', 'utils' are not available 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : dependencies 'timeDate', 'timeSeries', 'gdata', 'gplots', 'maps', 'zoo', 'DBI', 'RSQLite', 'stabledist', 'gss' are not available 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'fBasics' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'Hmisc' had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'Rserve' had non-zero exit status 6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'gmodels' had non-zero exit status 7: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'sandwich' had non-zero exit status 8: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'AnnotationDbi' had non-zero exit status 9: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'its' had non-zero exit status 10: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'vegan' had non-zero exit status 11: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'annotate' had non-zero exit status 12: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'annaffy' had non-zero exit status 13: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'genefilter' had non-zero exit status 14: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'geneplotter' had non-zero exit status 15: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... : installation of package 'simpleaffy' had non-zero exit status read_pgf.c: In function 'pgf_count_probeset_types': read_pgf.c:1265: warning: assignment from incompatible pointer type fintegrate.c: In function 'paramIntegration': fintegrate.c:350: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result gibbsEM.c: In function 'ecoEStep': gibbsEM.c:417: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result commonlib.c: In function 'blockWriteINT': commonlib.c:693: warning: format not a string literal and no format arguments commonlib.c: In function 'blockWriteBOOL': commonlib.c:712: warning: format not a string literal and no format arguments commonlib.c: In function 'blockWriteREAL': commonlib.c:734: warning: format not a string literal and no format arguments hbio.c: In function 'readHB_info': hbio.c:265: warning: cast from pointer to integer of different size hbio.c: In function 'readHB_header': hbio.c:307: warning: cast from pointer to integer of different size hbio.c:308: warning: cast from pointer to integer of different size hbio.c:343: warning: cast from pointer to integer of different size hbio.c:344: warning: cast from pointer to integer of different size hbio.c:345: warning: cast from pointer to integer of different size hbio.c:346: warning: cast from pointer to integer of different size hbio.c:303: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:311: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:321: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:333: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:351: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c: In function 'readHB_mat_double': hbio.c:420: warning: cast from pointer to integer of different size hbio.c:443: warning: cast from pointer to integer of different size hbio.c:472: warning: cast from pointer to integer of different size hbio.c:424: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:447: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:476: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c: In function 'readHB_aux_double': hbio.c:660: warning: cast from pointer to integer of different size hbio.c:627: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:638: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:645: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:665: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:693: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c: In function 'readHB_mat_char': hbio.c:974: warning: cast from pointer to integer of different size hbio.c:997: warning: cast from pointer to integer of different size hbio.c:1025: warning: cast from pointer to integer of different size hbio.c:978: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1001: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1029: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c: In function 'readHB_aux_char': hbio.c:1193: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1204: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1214: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1232: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c:1263: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result hbio.c: In function 'ParseRfmt': hbio.c:1539: warning: cast from pointer to integer of different size hbio.c:1549: warning: cast from pointer to integer of different size hbio.c:1553: warning: cast from pointer to integer of different size hbio.c: In function 'substr': hbio.c:1587: warning: cast from pointer to integer of different size lp_lib.c: In function 'read_XLI': lp_lib.c:5339: warning: implicit declaration of function 'Rprintf' lp_report.c: In function 'blockWriteLREAL': lp_report.c:167: warning: format not a string literal and no format arguments lp_report.c: In function 'blockWriteAMAT': lp_report.c:196: warning: format not a string literal and no format arguments lp_report.c: In function 'blockWriteBMAT': lp_report.c:261: warning: format not a string literal and no format arguments In file included from lp_rlp.c:97: lp_rlp.h: In function 'lp_yylex': lp_rlp.h:1012: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result lusol.c: In function 'LUSOL_report': lusol.c:626: warning: implicit declaration of function 'REvprintf' mmio.c: In function 'mm_read_unsymmetric_sparse': mmio.c:79: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result sparselib.c: In function 'resizeMatrix': sparselib.c:51: warning: ignoring return value of 'realloc', declared with attribute warn_unused_result albers.c:10: warning: type defaults to 'int' in declaration of 'southpole' The drop in erros might have been due to: # dpkg --install tex-common I don't know. It doesn't seem like I am too far off from running. Any help is greatly appreciated. Ron -- output of sessionInfo(): R version 2.7.1 (2008-06-23) x86_64-pc-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] annotate_1.5.16 Biobase_2.0.1 loaded via a namespace (and not attached): [1] KernSmooth_2.23-10 RColorBrewer_1.0-5 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Ron Eisler [guest] 2013-05-16T17:16:53 DEXSeq on two-exon genes: how to specify a formula without redundant terms http://comments.gmane.org/gmane.science.biology.informatics.conductor/48186 <pre>Hi DEXSeq users/developers, I have used DEXSeq successfuly for genes with many exons and really like the diagnostic/visualization plots that come with it. Recently though, for genes with two testable exons, I am getting the "Underdetermined model; cannot estimate dispersions." error. I figure this is due to redundant terms in my formula as shown in PS below. So my questions are: 1) Is there a way to specify the formula count ~ sample + (condition + batch) * exon so that redundant terms 'condition + batch' are removed? 2) If not, is it safe to change ncol(mm) to qr(mm)$rank (i.e., rank of model matrix to remove redundant terms) in this piece of code in estimateExonDispersionsForModelFrame: if (nrow(mm) &lt;= ncol(mm)) stop("Underdetermined model; cannot estimate dispersions. Maybe replicates have not been properly specified.") Would changing the code this way violate any assumptions of the DEXSeq model? Thank you, Mani PS: # condition + batch terms are redundant as sample term is already present! count ~ sample + (condition + batch) * exon condition batch Untr_biorep1 Untr biorep1 LPS_biorep1 LPS biorep1 Untr_biorep2 Untr biorep2 LPS_biorep2 LPS biorep2 [1] "(Intercept)" "sampleLPS_biorep2" "sampleUntr_biorep1" [4] "sampleUntr_biorep2" "conditionUntr" "batchbiorep2" [7] "exonE002" "conditionUntr:exonE002" "batchbiorep2:exonE002" _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Narayanan, Manikandan (NIH/NIAID) [E] 2013-05-16T15:14:26 DiffBind - error dba-count http://comments.gmane.org/gmane.science.biology.informatics.conductor/48180 <pre>Dear All, I come back to DiffBind and tried the new version, I am analyzing some 5hmc and mc Seq experiments in a HPC server. I have both biological replicates and two different peak callers, I first extracted consensus peakset for each replicate. I am facing some problems when I call dba.count I think I have some problems with the server, here is the message: *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call("croi_load_reads", as.character(bamfile), as.integer(insertLength)) 2: FUN("bed/sample_10_sorted_paired_RD_10.bed.gz"[[1L]], ...) 3: lapply(X = S, FUN = FUN, ...) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call &lt;- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call &lt;- sys.call(-4L) dcall &lt;- deparse(call)[1L] prefix &lt;- paste("Error in", dcall, ": ") LONG &lt;- 75L msg &lt;- conditionMessage(e) sm &lt;- strsplit(msg, "\n")[[1L]] w &lt;- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w &lt;- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w &gt; LONG) prefix &lt;- paste0(prefix, "\n ") } else prefix &lt;- "Error : " msg &lt;- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent &amp;&amp; identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 10: FUN(1:12[[12L]], ...) 11: lapply(seq_len(cores), inner.do) 12: mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) 13: config$lapplyFun(config, params, arglist, fn, ...) 14: dba.parallel.lapply(pv$config, params, todo, pv.getCounts, bed, insertLength, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode, singleEnd, scanbamparam) 15: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, bLog = bLog, insertLength = insertLength, bOnlyCounts = T, bCalledMasks = bCalledMasks, minMaxval = filter, bParallel = bParallel, bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl, filterFun = filterFun, bLowMem = bLowMem) 16: dba.count(testsave, peaks = conspeaks) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Any suggestion? Thanks again, Paolo [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Paolo Kunderfranco 2013-05-16T10:27:32 an error in HeatPlus package http://comments.gmane.org/gmane.science.biology.informatics.conductor/48175 <pre>Hi, I'm trying to use the HeatPlus package, but I'm getting the following error when I tried to use annHeatmap or annHeatmap 2 functions: usemap1 &lt;- annHeatmap(mat, ann) Error: could not find function "annHeatmap" I have followed the instructions from the manual: source("http://bioconductor.org/biocLite.R") biocLite("Heatplus") and the example: ## Default method set.seed(219) mat = matrix(rnorm(100), ncol=5) ann = data.frame(Class=c("A","A","B","A","B")) map1 = annHeatmap(mat, ann) I'd appreciate any help, or if there is any other package to produce heat maps, please let me know. Thank you, Adriana Postdoc U Maryland [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Adriana Munoz 2013-05-16T03:38:06 meme/fimo output parser? http://comments.gmane.org/gmane.science.biology.informatics.conductor/48174 <pre>does anyone have code for parsing the XML output of fimo into GRanges? [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> Vincent Carey 2013-05-16T02:44:54 timecourse for RNA-seq data http://comments.gmane.org/gmane.science.biology.informatics.conductor/48173 <pre> Dear mailing list, I have only one replicate of an RNA-seq time course experiment. I have transcript count, RPKM nomalized gene count, gene expression values, exon count, and other data available at my disposal. For example, the ratio of unique to total transcript reads for each gene. This is a timecourse array with 3 experimental groups, and can be considered a longitudinal study. The current timecourse package calls for RMA-normalized log2 data. I'm not a programmer, but, will the source code accept my count data to give a reliable output? If possible, can you suggest how to proceed? Regards, Franklin -- output of sessionInfo(): N/A -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor </pre> FRANKLIN JOHNSON [guest] 2013-05-16T02:41:15 Search Engine Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.informatics.conductor