http://blog.gmane.org/gmane.science.biology.informatics.conductor hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.science.biology.informatics.conductor/48792 <pre>Hi, I am trying to make a pd.info package for the Affy Primeview array, but I get an error. Thanks for any help! Cheers, Max This is my code: library(pdInfoBuilder) cdf &lt;- list.files( pathAnnotPr, pattern = ".cdf", full.names = TRUE ) cel &lt;- list.files( pathC, pattern = ".CEL", full.names = TRUE )[1] # take first array tab &lt;- list.files(pathAnnotPr, pattern = "_tab", full.names = TRUE) seed &lt;- new("AffyExpressionPDInfoPkgSeed", cdfFile = cdf, celFile = cel, tabSeqFile = tab, author = "xx", email = "xx", biocViews = "AnnotationData", genomebuild = "hg19", organism = "Human", species = "Homo Sapiens", url = "xx" ) makePdInfoPackage( seed, destDir = "." ) Which produces this output/error (although a pd.primeview directory is created): ============================================================================ ==== Building annotation package for Affymetrix Expression array CDF...............: PrimeView.cdf CEL.........</pre> Max Kauer 2013-06-18T13:25:11 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48790 <pre>Dear all, i have three excel files and also saved as object and i am trying to extract common genes sorted according to the ID in R . Can anyone help me how to do it. Thanks Nikul </pre> Nikul Soni 2013-06-18T12:27:08 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48786 <pre> [[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> Margaret Linan 2013-06-18T06:43:11 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48785 <pre>Abhi, Great to hear from someone using ReportingTools "in the wild". I'm glad you are finding it useful. I only see two requests in your message, though you mentioned having 3. I will answer the one about images first. It is entirely possible to have multiple images per row. The "adding plots or links to a report table" section of the basic ReportingTools vignette describes how to add or customize columns within a table, including columns whose contents are images. Having multiple images per row is as simple as adding multiple image columns to the table. As for aligning the entire report, formal support for custom CSS is a feature which we hope to have in the next version of ReportingTools, but didn't make it into this one. That said, you have both full control over the publishing methods and direct access to the DOM so I believe there are various things you can do to override the alignment of a specific table (or all tables, etc) with the current version. I'm not on a computer that has ReportingTools i</pre> Gabriel Becker 2013-06-18T05:53:02 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48783 <pre>Dear Simon, Alejandro, etc I am trying to get the associated gene name printed next to the gene id column that is displayed on the HTML report created by the DEXSeqHTML function. I am aware there are options within the function, but I do not know how to use them to get the result that I am looking for. For example I do not know how to create a mart class object or use the attributes option. I have tried to google all of my concerns but haven't found a good example or explanation yet. Please help? Thanks, Margaret Linan [[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> Margaret Linan 2013-06-18T03:06:14 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48782 <pre> hi all, the data set i have consists of x which is a matrix of 39 cancer patients [rows] and 2000 gene names [colmns]. each cell is the value of the gene for a particular patient. there are two types of cancer people representedas factor y. here is the code: library(e1071) #load database db &lt;- read.csv(file="databases\\colon-cancer\\colon-cancer.csv",head=FALSE,sep=",") x = as.matrix(db[,1:(ncol(db)-1)]) y = as.factor(db[,ncol(db)]) svmModel = svm(x, y, cost = 10, cachesize=500, scale=F, type="C-classification", kernel="linear" ) my question is :to plot the svm model i need to plot 2 vaiables as y axis and x axis....but according to the nature of my dataset i have about 2000 variables?? does that mean i have to plot only two?? or is there a way to plot all of the 2000 and beable to show how the svm model classify the dataset. -- output of sessionInfo(): sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Arabic_Saudi Arabia.12</pre> nofe [guest] 2013-06-17T23:50:34 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48780 <pre>Hi Guys Now that I am able to create basic reports which already are a great time saver. I am wondering do I have some flexibility to decide where to render images and some page formatting options. For example I have three specific requirements at this point. 1. Left align the whole page. Currently a rendered table is centered cutting the displayed text as it is horizontally broad 2. put multiple images in a single row; in other words put 2-3 images side by side in a row. Thanks! -Abhi _______________________________________________ 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> Abhishek Pratap 2013-06-17T22:45:33 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48775 <pre>According to here: https://stat.ethz.ch/pipermail/bioc-devel/2009-December/002061.html the AnnotationDbi pacakge promotes as.list to an S4 generic that knows about Bimap objects and such. However, after loading AnnotationDbi in my R, I get: &gt; showMethods("as.list") Function "as.list": &lt;not an S4 generic function&gt; Furthermore, when loading the annotate package, I get: &gt; library(annotate) Warning message: In namespaceImportMethods(ns, loadNamespace(j &lt;- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "as.list" from package "AnnotationDbi" (malformed exports?) And now all the functions from annotate, such as getSYMBOL, lookUp, etc., fail with an error, exemplified by the following snippet from the help text of lookUp: &gt; library("hgu95av2.db") &gt; library("GO.db") &gt; &gt; data(sample.ExpressionSet) &gt; gN &lt;- featureNames(sample.ExpressionSet)[100:105] &gt; lookUp(gN, "hgu95av2", "SYMBOL") Error in as.list.default(envir) : no method for coercing this S4 </pre> Ryan C. Thompson 2013-06-17T22:23:54 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48773 <pre> If you are having trouble reading this email, view the Web Version. EMBO Practical Course Bioinformatics and statistics for large-scale data 17–22 November 2013 | Yantian District, China Interested in attending? Visit the website: http://events.embo.org/13-large-scale-data Register by: 20 September 2013 Visit our Facebook page: https://www.facebook.com/events/445948875502253/ Bronagh Carey Administrative Officer EMBO Courses &amp; Workshops and Global Activities Meyerhofstrasse 1 D-69117 Heidelberg Germany Tel: +49 (0) 6221 8891 409 [[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> Wolfgang Huber 2013-06-17T18:37:01 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48768 <pre> Thank you in advance for answering my question about limma package! The function read.ilmn() reads in probe_file.txt and control_probe_file.txt seperately for illumina microarray data. What if my illumina Gene Expression BeadChip data look like below? How can I use read.ilmn and follow the steps described in limma user guide 15.3? It is just one file containing the columns: TargetID ProbeID sample1_1 sample1_2 sample2_1 sample2_2 control1_1 control1_2 control2_1 control2_2 The partial real data look like below: Illumina Inc. GenomeStudio version 1.9.0 Normalization = none Array Content = HumanHT-12_V4_0_R1_15002873_B.bgx.xml……. TargetIDProbeIDMIN_Signal-A253-1AVG_Signal-A253-1MAX_Signal-A253-1NARRAYS-A253-1ARRAY_STDEV-A253-1BEAD_STDEV-A253-1Avg_NBEADS-A253-1Detection-A253-1MIN_Signal-A253-2AVG_Signal-A253-2MAX_Signal-A253-2NARRAYS-A253-2ARRAY_STDEV-A253-2BEAD_STDEV-A253-2 .....then control 1, 2, ... 7A5645025586.386.386.31NaN7.886190.8766279.2</pre> xiayu [guest] 2013-06-17T14:39:44 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48766 <pre>To whom it may concern. Hello, I am new in microarray data analysis. recently I want to use Limma to find different expressed genes between grade I and grade III, which you could see from the annotation file. but when I use the R code below to do this, I only got two different expressed genes, could anybody tell me why? Is there anything wrong with my code? thank you in advance! and the data is available on line.http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2990.   Best regards, yongzi Best wishes to you! ====================================================== Yong-Zi Chen, Ph.D.   Tianjin Cancer Institute Tianjin Medical University Cancer Institute and Hospital Huan-Hu-Xi Road, Ti-Yuan-Bei, He-Xi District Tianjin300060, P.R. China Phone&amp;Fax:   0086-022-23340123geo_accnsample_nametreatmentdatasetgradenodesizeageerevent.rfstime.rfsevent.dmfstime.dmfs GSM65753KIU_105B13noneKJ125101.346107.32876712307.328767123 GSM65754KIU_106B55noneKJ12510637111.1671232</pre> yongzi chen 2013-06-17T01:31:20 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48765 <pre>Hi, I am getting incorrect feature annotation data when loading a dataset from GPL4133. The feature data looks like this: head(fData(eset)[, 1:2]) ID COL 12 12 266 NA &lt;NA&gt; &lt;NA&gt; NA.1 &lt;NA&gt; &lt;NA&gt; 15 15 266 16 16 266 NA.2 &lt;NA&gt; &lt;NA&gt; This possibly also results in having less features in the final expression matrix, if it is at some point restricted to feature names matching the ones in the loaded annotation data. The real issue here seems to be with the soft file being badly formatted, with lines having double quotes where there should not be: 12 266 148 A_24_P66027 A_24_P66027 FALSE NM_004900 NM_004900 9582 APOBEC3B apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B" Hs.226307 ... Looking at the way GEOquery loads the annotation soft files, we see that they are read using `quote="\""`, which clearly returns a messed up data.frame. So: - the real issue should be solved by GEO teams (in Cc), by re-generating the soft files</pre> Renaud Gaujoux 2013-06-17T11:09:27 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48764 <pre>lvqv http://attelonsnous.fr/jqtxigse/RNDCHR,3,15%/jknaxvtuguls/vbjhl/anrpzdffyv.htm urzl [[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> carol white 2013-06-17T10:00:51 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48762 <pre> Dear Maintainer, Thanks for this package. It is great and very useful. I am (6) Analyzing and Visualizing Results, however, I cannot seem to adjust the legend in the EIC plot. I tried using the logical, legend=FALSE, as well as alternatives, but my approaches did not work. Is there not an argument used by diffreport function to not print the legend? The legend that does print is too large as I have 95 files, and covers a large area of the EIC plot. Additionally, if my arguments in diffreport are such that class1 = levels(sampclass(object))[1], class2 = level(sampclass(object)[2], the diffreport reads and prints the appropriate samples in each sampclass(object), 3 samples per class [06041319.mzdata 06041320.mzdata 06071324.mzdata &lt;-class[1] samples; 06041303.mzdata 06071321.mzdata 06071322.mzdata &lt;- class[2] sample], although the output file has all 95 samples. 1) How is it the intensity is being adjusted in the other 93 samples, when in diffreport function, I compare 2 different classes? 2) How can</pre> FRANKLIN JOHNSON [guest] 2013-06-17T01:14:22 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48761 <pre>Hi I seem to be getting an error when trying to replicate ReportingTools example of putting a plot on the webpage both using the one generated in R and an external image. Not sure if the error has anything to do with versions. Session info included too. ### #plot generated within R ### my.df &lt;- data.frame(EGID = c("103", "104", "105", "106", "107"), RPKM = c(4, 5, 3, 100, 75), DE = c("Yes", "Yes", "No", "No", "No")) plot(my.df$EGID, my.df$RPKM, xlab="EGID",ylab="RPKM", main="Scatter plot of RPKMs", col="blue") scatterPlot &lt;- recordPlot() library(lattice) barPlot &lt;- barchart(my.df$RPKM~my.df$EGID) ##lattice plots behave slightly differently htmlRep3 &lt;- HTMLReport(shortName = "my_html_file3", title="Adding a plot directly to the page",reportDirectory = "./reports") publish(scatterPlot, htmlRep3, name = "scatterPlot") Error in as(object, "data.frame") : no method or default for coercing “recordedplot” to “data.frame” ##### ****Also when I try to put a pr</pre> Abhishek Pratap 2013-06-16T22:50:08 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48754 <pre> Hi, I am trying to extracts mate pairs that are mapped to a particular chromosome (say chr1). The construction of my which() function is not returning what I need. May be I am missing something in constructing it. bf.data= readGappedAlignments(bam_files, param=ScanBamParam(what=scanBamWhat())) mate.pairs=table(mcols(bf.data)$qname) onlyPairs=names(mate.pairs)[mate.pairs==2] mappedPairs=bf.data[mcols(bf.data)$qname %in% onlyPairs] mate1=mappedPairs[c(T,F)] mate2=mappedPairs[c(F,T)] isSameCzome= (seqnames(mate1)==seqnames(mate2)) chrnames=seqnames(mate1[which(seqnames(mate1[isSameCzome])=="chr1")]) With the last statement I am intending to extract mate1 that are mapped to chr1. So I expect chrnames to contain only chr1, but it returns all other chromosomes and not just for chr1. Is there something I am missing in the way I have written the which statement? Thanks for your help. Cheers../Murli -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-redhat-linux-gnu (64-bit) loca</pre> Murli Nair [guest] 2013-06-15T17:17:27 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48749 <pre>Dear list, I have recently come along the ComBat function from the sva package. I am currently analyzing Agilent one-color microarray data and I had strong batch effects. No normalization method could get rid of this effect and the data clustering showed it clearly. The reasons for this batch effects are multiple, but the bottom line is that I want to control them. Data experiment: 6 types of samples named: pp4, pp2, p4, p2, p0 and pn, with 3, 2, 3, 3, 2, and 1 replica respectively. There are a total of 5 batches. So I did the following pipeline: - normalize the data using quantile - apply ComBat on the data For ComBat, I use the following file, hereafter called "phenoBatches.txt" that contains the info on batches and covariates: "phenoBatches.txt" sample outcome batch cancer 1 pp4_1 14430 pp4 2 pp2_1 14430 pp2 3 p4_1 14407 p4 4 p2_1 14407 p2 5 pp4_2 10957 pp4 6 p4_2 10957 p4 7 p2_2 10957 p2 8 pp4_3 12957 pp4 9 p4_</pre> Alexandra Popa 2013-06-14T15:21:53 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48748 <pre>Hi, I have a question about concerning the number of differentially expressed probes after batch combination, using ComBat from 'sva'. I have 2 data sets: one containing around 250 samples that correspond to around 50 groups, another one containing 10 samples corresponding to 2 groups (let me call them Batch2_Group1, Batch2_Group2). One of the 2 group labels in the second batch (Batch2_Group2) also exists in the first batch, so there is no confounding situation here. Before batch correction the 2 data sets cluster by batch, not by group. I used ComBat from the R/Bioconductor package 'sva' to correct for this, using a model matrix to accommodate the overlapping groups between the 2 batches and setting par.prior=TRUE, i.e. using parametric adjustment. After the batch correction the samples cluster perfectly by group, not by batch any longer. I do notice, however, that the number of differentially expressed probes between Batch2_Group1 and Batch2_Group2 changes dramatically with data combination. Within Ba</pre> Michaela Oswald 2013-06-14T14:48:45 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48747 <pre>Hello,Dear Madam, Sir,I am a novice student of R, I'm in a training graduation and I encountered a problem on R (version 2.15.3) for the analysis of 'hugene21st' Affymetrix chips type; by installing the 'hugene21st' package with the controls:source ("http://www.bioconductor.org/biocLite.R")biocLite ("hugene21st")I have this error message: package 'hugene21st' is not available (for R Version 2.15.3) what to do to fix this problem pleas, or what version of R should be used to treat these chips. cordially; Chagdal Madiha SITN Master-2 : Statistics, Computer and Digital Techniques Claude Bernard Lyon-1 University [[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> chm chag 2013-06-14T10:12:32 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48745 <pre> Hello, I'm interested in using the pairwiseAlignment function in Biostrings to perform simple alignments of short sequences. I noticed that even the global alignment mode returns an alignment with gapped ends trimmed off. For example: Global PairwiseAlignmentsSingleSubject (1 of 1) pattern: [3] GG subject: [1] GG score: -32.03649 Is it possible to obtain the complete alignment including the (possibly) gapped ends? In this case, that would be: --GG-- AAGGAA For my purposes, having the complete gapped alignment is important. My question seems related to a previous post: https://stat.ethz.ch/pipermail/bioconductor/2012-February/043577.html Thank you in advance. Best wishes, Rob </pre> Robert K.Bradley [guest] 2013-06-15T02:57:30 http://comments.gmane.org/gmane.science.biology.informatics.conductor/48744 <pre>All, I am attempting to use snapCGH for CGH data. I was able to read in the generic format with limma, however, I am unable to figure out where to get the data for read.clonesinfo. Any suggestions on where to look. Thanks, Juliet [[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> Juliet Hannah 2013-06-14T22:51:40 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.informatics.conductor