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/18014 Call for participants BIRD'08 2nd International Conference on Bioinformatics Research and Development www.birdconf.org <http://www.birdconf.org> Technical University of Vienna, Austria July 7-9, 2008 Best regards Roland Wagner Prof. Roland Wagner 2008-05-17T12:51:27 http://comments.gmane.org/gmane.science.biology.informatics.conductor/18010 Hello, Im running R 2.5.0 When I load the R package GEOquery, I am getting the following error: the part of the args list of 'list' being evaluated was: (header = list(), ) Error in makeClassRepresentation(Class, properties, superClasses, prototype, : element 2 is empty Error : unable to load R code in package 'GEOquery' Error: package/namespace load failed for 'GEOquery' Seems to have installed fine, or maybe not. package 'GEOquery' successfully unpacked and MD5 sums checked updating HTML package descriptions Any insight? Thanks! al({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) the part of the args list of 'list' being evaluated was: (header = list(), ) Error in makeClassRepresentation(Class, properties, superClasses, prototype, : element 2 is empty Error : unable to load R code in package 'GEOquery' Error: package/namespace load failed for 'GEOquery' Justin Balko, PharmD Graduate Student Dept of Pharmaceutical Sciences University of Kentucky 441 College of Pharmacy 725 Rose St Lexington, KY 40536 859-257-2577 STATEMENT OF CONFIDENTIALITY\ The contents of this email...{{dropped:14}} _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Balko, Justin M 2008-05-16T20:58:56 http://comments.gmane.org/gmane.science.biology.informatics.conductor/18007 Hi, I'm trying to use gcrma with affinity.source= "local", and a predefined set of NCprobes with gcrma v. 2.12.0. However, I'm running into problems with the sub-function base.profiles.nc. I think that where it says: if (length(seqs) < length(NCprobe)) { cat("\nNote: some of your negative control probes do not have sequence information\n") subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename), xy2indices(p$x, p$y + 1), cdf = cdfpackagename), NCprobe) subIndex2 <- subIndex2[!is.na(subIndex2)] bgy <- bgy[!is.na(subIndex1), ] } isn't is supposed to be: if (length(seqs) < length(NCprobe)) { cat("\nNote: some of your negative control probes do not have sequence information\n") subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename), xy2indices(p$x, p$y + 1, cdf = cdfpackagename)), # moving the ")" here NCprobe) subIndex2 <- subIndex2[!is.na(subIndex2)] bgy <- bgy[!is.na(subIndex1), ] } Thanks \Heidi R version 2.7.0 Under development (unstable) (2008-02-12 r44439) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10stv1probe_0.0.1 biomaRt_1.13.10 RCurl_0.8-3 [4] arrayQualityMetrics_1.4.18 beadarray_1.7.3 latticeExtra_0.3-1 [7] simpleaffy_2.15.02 affyPLM_1.15.5 RColorBrewer_1.0-2 [10] genefilter_1.17.12 survival_2.34 mogene10stv1cdf_1.18.0 [13] geneplotter_1.17.7 annotate_1.17.12 xtable_1.5-2 [16] AnnotationDbi_1.2.0 RSQLite_0.6-7 DBI_0.2-4 [19] gcrma_2.12.0 matchprobes_1.11.0 vsn_3.4.13 [22] limma_2.13.4 lattice_0.17-4 affy_1.17.3 [25] preprocessCore_1.1.5 affyio_1.7.17 Biobase_1.99.4 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 XML_1.93-2 _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Heidi Dvinge 2008-05-16T17:48:31 http://comments.gmane.org/gmane.science.biology.informatics.conductor/18005 Hello, a short question. How would one manage to have the color range centred around 0 instead of assigning the extreme colors (say red and green) to the lowest and largest value? Black should be at "0" and not at the mean value between the largest and the smallest value. I need to compare different heatmaps. Thanks for any suggestion Hartmut Here some simple Data: mdat <- matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201 09742826,0.0908534304511135,-0.500217879852688,-0.182786075741673,-0.248 107861595691,-0.362157939675895),ncol=3,nrow=3,dimnames=list(c("C1","C2" ,"C3"),c("T1","T2","T3"))) heatmap.2(mdat,Rowv=NULL,Colv="Rowv", scale="none",col=greenred(75),key=TRUE, symkey=FALSE, density.info="none", trace="none",dendrogram="none") [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Hartmut Scheel 2008-05-16T15:51:12 http://comments.gmane.org/gmane.science.biology.informatics.conductor/18004 Hello BioC community: I am having trouble with lumiMouseV1. I am able to go from ID -> ENTREZID via lumiMouseV1ENTREZID: lumiMouseV1ENTREZID,ifnotfound=NA) $iSh39ilew_g4tR.A18 [1] 78928 $`GI_10304988-S` [1] NA $oS6QgIgopJKKQ4S9Ko [1] 16728 $`GI_12963686-S` [1] NA $`GI_12963764-I` [1] NA $`GI_13385605-S` [1] NA However, when I do the same for ID -> GO, every entry is NA. $iSh39ilew_g4tR.A18 [1] NA $`GI_10304988-S` [1] NA $oS6QgIgopJKKQ4S9Ko [1] NA $`GI_12963686-S` [1] NA $`GI_12963764-I` [1] NA $`GI_13385605-S` [1] NA (This is just a snippet, but they are all NA) Looking at the info for LumiMouseV1() shows Quality control information for lumiMouseV1 Date built: Created: Fri Sep 14 10:29:15 2007 Number of probes: 39562 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: lumiMouseV1ACCNUM found 39562 of 39562 lumiMouseV1CHRLOC found 27910 of 39562 lumiMouseV1CHR found 30304 of 39562 lumiMouseV1ENTREZID found 30322 of 39562 lumiMouseV1ENZYME found 3017 of 39562 lumiMouseV1GENENAME found 30322 of 39562 lumiMouseV1GO found 25323 of 39562 lumiMouseV1MAP found 28678 of 39562 lumiMouseV1PATH found 6548 of 39562 lumiMouseV1PMID found 29523 of 39562 lumiMouseV1REFSEQ found 29944 of 39562 lumiMouseV1SUMFUNC found 0 of 39562 lumiMouseV1SYMBOL found 30322 of 39562 lumiMouseV1UNIGENE found 29391 of 39562 Mappings found for non-probe based rda files: lumiMouseV1CHRLENGTHS found 21 lumiMouseV1ENZYME2PROBE found 758 lumiMouseV1GO2ALLPROBES found 7796 lumiMouseV1GO2PROBE found 5614 lumiMouseV1ORGANISM found 1 lumiMouseV1PATH2PROBE found 192 lumiMouseV1PFAM found 23763 lumiMouseV1PMID2PROBE found 104537 lumiMouseV1PROSITE found 16873 Mappings from Illumina Identifiers to nuIDs: lumiMouseV1PROBEID2NUID: from Illumina Probe Id to nuID lumiMouseV1TARGETID2NUID: from Illumina Target Id to nuID It appear that the there is nothing in lumiMouseV1GO. If you convert it to a list, it just shows list(). This doesn't happen with lumiMouseV1ENTREZID. Looking at the lengths shows this. [1] 39562 [1] 0 I have tried the exact same thing with lumiHumanV2GO (and different data set), and it works. So I think I have the right idea, but may be overlooking something obvious. Any help would be greatly appreciated. Thanks, Wade J. Wade Davis, Ph.D. Assistant Professor of Biostatistics University of Missouri Below is my session info. R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] lumiHumanV2_1.3.1 illuminaMousev1p1_1.4.0 illuminaMousev1_1.4.0 affycoretools_1.10.2 [5] gcrma_2.10.0 matchprobes_1.10.0 biomaRt_1.12.2 RCurl_0.8-1 [9] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 survival_2.34 [13] RBGL_1.14.0 GO.db_2.0.2 graph_1.16.1 annaffy_1.10.1 [17] GO_2.0.1 KEGG_2.0.1 XML_1.93-2.1 limma_2.12.0 [21] lumiMouseV1_1.3.1 lumi_1.4.0 annotate_1.16.1 xtable_1.5-2 [25] AnnotationDbi_1.0.6 RSQLite_0.6-7 DBI_0.2-4 mgcv_1.3-29 [29] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.3 [33] RWinEdt_1.7-9 loaded via a namespace (and not attached): [1] cluster_1.11.9 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Davis, Wade 2008-05-16T14:49:56 http://comments.gmane.org/gmane.science.biology.informatics.conductor/18000 I am a satistified user of affyQCReport and want to make sure that I include the appropriate citations in a paper I am submitting. As this package is sort of a wrapper for some other packages and the vignette does not include any references beyond that of Gautier, et al, which describes the affy package, could someone be kind enough to supply me with the appropriate citations? In general, it is sort of a pet peeve of mine that developers rightly want their work cited, but too often I feel that the citation information on the help(package == "foo") page is imcomplete. Would it be presumtuous to ask for developers to include a handy list of citations for their packages, package dependencies, etc. as part of the general help page for their package? I don't know what the official R/BioC policy is on this, but it would be extremely helpful both to users and those whose original ideas are incorporated into R/BioC. And, if I"ve missed something obvious, point me in the right direction, spank me with a wet noodle and accept my apologies. Thanks, Mark Mark Kimpel 2008-05-16T00:34:47 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17988 dear list members, i'm having a problem installing the biomaRt package on my linux machine, due to the fact of a compilation error with RCurl. i am using R 2.6.2 on fedora 7, and this is the output i get: gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c base64.c -o base64.o In file included from base64.c:1: Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t? base64.c: In function ?R_base64_decode?: base64.c:25: warning: pointer targets in assignment differ in signedness base64.c:39: warning: pointer targets in passing argument 1 of ?Rf_mkString? differ in signedness base64.c: In function ?R_base64_encode?: base64.c:60: warning: pointer targets in assignment differ in signedness make: *** [base64.o] Error 1 as far as i know i have all the necessary libraries installed: $ yum list installed | grep libxml libxml2.i386 2.6.31-1.fc7 installed libxml2-devel.i386 2.6.31-1.fc7 installed libxml2-python.i386 2.6.31-1.fc7 installed perl-libxml-perl.noarch 0.08-1.2.1 installed $ yum list installed | grep curl curl.i386 7.16.4-1.fc7 installed curl-devel.i386 7.16.4-1.fc7 installed python-pycurl.i386 7.16.0-0.1.20061207.fc installed as i am not an expert in linux stuff, i was wondering if there could be any other missing libraries? any other ideas? cheers martin [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor martin sikora 2008-05-15T15:56:06 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17987 Hi Any suggestions how to map gene symbols to mouse EntrezId(preffered) or Affy. mapping to Entez apparently is not supported by GSEABase Error in .mapIdentifiers_isMappable(from, to) : unable to map from 'Symbol' to 'EntrezId' neither GeneIdentifierType has annotation Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose = verbose)) : error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection' Mapping to Affys works for human, but not for mouse GeneSetCollection names: chr5q23, chr16q24 (2 total) unique identifiers: 35089_at, 35090_g_at, ..., 35807_at (79 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: BroadCollection (1 total) GeneSetCollection names: chr5q23, chr16q24 (2 total) unique identifiers: (0 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: BroadCollection (1 total) Thanks Vladimir Morozov [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Vladimir Morozov 2008-05-15T15:49:18 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17985 Hi, I get error reading the last vesrsion of Broad msigdb . Is it supposed to work? Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'c5' 6: stop("'getBroadSets' failed to create gene sets:\n ", conditionMessage(err), call. = FALSE) 5: value[[3]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ geneSets <- unlist(mapply(.fromXML, uri, "//GENESET", factories, SIMPLIFY = FALSE, USE.NAMES = FALSE)) }, error = function(err) { stop("'getBroadSets' failed to create gene sets:\n ", conditionMessage(err), call. = FALSE) }) 1: getBroadSets("/data/PathDB/msigdb_v2.5.xml") Package: GSEABase Type: Package Title: Gene set enrichment data structures and methods Version: 1.2.0 Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer: Biocore Team c/o BioC user list <bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org> Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). License: Artistic-2.0 Depends: R (>= 2.6.0), methods, AnnotationDbi, Biobase, annotate Suggests: Ruuid, hgu95av2.db, GO.db, org.Hs.eg.db Imports: methods, XML, graph LazyLoad: yes biocViews: Infrastructure, Statistics Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R methods-CollectionType.R methods-ExpressionSet.R methods-GeneColorSet.R methods-GeneIdentifierType.R methods-GeneSet.R methods-GeneSetCollection.R methods-OBOCollection.R zzz.R Packaged: Wed Apr 30 02:43:40 2008; biocbuild Built: R 2.7.0; ; 2008-05-14 16:18:51; unix Vladimir Morozov 2008-05-15T14:52:26 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17984 Hi all, I have just started using the GenomeGraphs package, which I think is a really good piece of software :) I am using the package to plot expression values across a genomic region. However, it seems to plot all points on the same "track" in the same colour? I was wondering if it is possible to use different colours to highlight particular probes I am interesting in, (or use different plotting characters). I thought something like: dp=DisplayPars(color=c("red","blue")) might work, but it just produced one colour. Apologies if there is already the ability to do this, but I didn't see anything so far. Many thanks, Mark _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Mark Dunning 2008-05-15T14:39:28 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17980 Dear all, I use R "XML" package to parse DTD files, however, it seems that parseDTD function cannot extract "entity" information. ================ dtdFile <- system.file("exampleData","foo.dtd", package="XML") foo.dtd <- parseDTD(dtdFile) foo.dtd$entities ###NULL dtdEntity("img", foo.dtd) ###NULL packageDescription("XML")$Version ### "1.95-2" ================ sessionInfo ================= R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] XML_1.95-2 loaded via a namespace (and not attached): [1] tools_2.7.0 ================= LiGang [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor LiGang 2008-05-15T09:01:24 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17979 The prospective business firm searches for new employees If you have 5 free hours each week, a little experience in internet and free phone to which we can contact you, you have possibility to commence cooperation with us and get more than 2000 US dollars If you are interested in our proposition, contact us by e-mail: groupi-y7T6Qt9oWrYvJsYlp49lxw< at >public.gmane.org and we will send you further information. Best regards RINKAJA LTD _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Konstanze guler 2008-05-15T08:09:30 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17978 when I type the command Data<-ReadAffy() Error: cannot allocate vector of size 831.6 Mb my system is ArchLinux ,and free the memory infomation like this total used free shared buffers cached Mem: 2075116 1980384 94732 0 94840 1030020 -/+ buffers/cache: 855524 1219592 Swap: 2048248 226472 1821776 what can I do if I want to read the cel files one time? thans . melody [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor xiong mody0911 2008-05-15T02:30:02 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17968 Hello list, In *Schuster et al. 2007 (http://genomebiology.com/2007/8/6/R125) a method is presented allowing to correct *MAS5 present/absent calls based on gcRMA transformed PM threshold values. The R script is available in sup data at http://genomebiology.com/content/supplementary/gb-2007-8-6-r125-s1.txt When trying to run it on my data I am faced to an error: > data AffyBatch object size of arrays=854x854 features (11 kb) cdf=gnGNF1Musa (36182 affyids) number of samples=16 number of genes=36182 annotation=gngnf1musa notes= > ai <- compute.affinities.local(data, Array=NULL) Adjusting for optical effect................Done. Computing base-position profiles for probe affinitiesErreur dans complementSeq(seqs, start = 13, stop = 13) : Character N does not code for a nucleic acid. I tried with other platforms (e.g. mgu74av2) and this works. So I guess this is due to an error in the annotation package gngnf1musa. I installed this package (custom array affymetrix) made available by Cei Abreu-Goodger (http://article.gmane.org/gmane.science.biology.informatics.conductor/13659) at ftp://ftp.sanger.ac.uk/pub/cei/gngnf1_R_packages.tar.gz What can be wrong? Then I tried: > ai <- compute.affinities(cdfName(data)) Computing affinities.Done. This worked. However I am not sure it is doing the same thing (Adjusting for optical effect? Computing base-position profiles for probe affinities?) What is the difference between compute.affinities and compute.affinities.local? Thanks for your help to clarify this. Julien > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] gngnf1musaprobe_1.8.1 gngnf1musacdf_1.14.0 gcrma_2.12.0 [4] matchprobes_1.12.0 affy_1.18.0 preprocessCore_1.2.0 [7] affyio_1.8.0 Biobase_2.0.1 Julien Roux 2008-05-14T15:26:28 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17967 Hi, everyone Currently I am trying to processing affymetrix exon ST array data, but I can not find more detailed information online. It looks the latest ST arrays only output grd and flc files. I can find that the grd files contain information about how to grid the acquisition files based on affymetrix docs, but have no idea about flc files. In general, you know, the data are stored in CEL files, but I don't know which one contains information that are included in old CEL files. so any comment? Or where can I find a tutorial about this case? Thanks a lot! Gilbert [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor peach gil 2008-05-14T15:24:34 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17961 Hello all, I am a PhD student at University of Pisa. I frequently use LIMMA package to handle gene expression microarray data. I have a question about spot copies management by LIMMA. I know that LIMMA needs all spots on the array are in the same number of copy ( e.g. each spot in double ). In my research group It is just starting a project in wich we use Agilent microarrays (so high density microarrays) and on these arrays there is only a block of probes, positioned in a random fashion, in more than one spot for each probe. Moreover there is not the same number of copies for each probe in this block. Is LIMMA able to manage this situation? That is, is LIMMA able to use this kind of random replicated spots to perform a quality control procedure, to fit the linear model and to produce a unique fold change value for this probe? Can I use any kind of strategy to solve this problem? Does It exists a free package that does this? Thank you very much for any information about this topic. Best Regards Erika Melissari [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Erika Melissari 2008-05-14T10:21:18 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17960 Hi! I'd welcome some help on creating a design matrix for a time-course experiment. I have 7 time points (0,3,6,9,12,24,27 hours) with three technical replicates at each time point. Cy3 is the untreated, Cy5 is the treated sample on each chip. There is an example in the limma user guide for time course experiments, but I'm still a bit confused about design and contrast matrices. Thanks in advance, Endre Sebestyen _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Endre Sebestyen 2008-05-14T10:12:19 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17959 Hi to all, I've done a simple web interface to help to use the BioC annotations packages also for users who are not familiar with R. It uses the AnnotationDbi packages (e.g: every *.db.. hgu95av2.db, hgug4112a etc..). so also for customs arrays we can make the package with makeHUMANCHIP_DB or whatever and add it in the tool. Also it uses RApache http://biostat.mc.vanderbilt.edu/rapache/ and R-2.7.0 You can download it here: http://sourceforge.net/projects/annotweb-bioc/ Basic instructions are in the "INSTALL" file inside the package. I hope you find it useful Best regards Francesco [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Francesco Favero 2008-05-14T09:19:31 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17958 Dear All, An email was sent to this mailing list accidentally. Will you all please be able to delete it? Sorry and thanks heaps Yogi ________________________ Yoganand Sundaravadanam Bioinformatics Officer Australian Genome Research Facility Ltd The Walter and Eliza Hall Institute 1G Royal Pde Parkville VIC 3050 Phone: +61 3 9345 2682 Fax: +61 3 9345 2678 Email: yogi.sundarvadanam-P5e5sBhJi5y6c6uEtOJ/EA< at >public.gmane.org Web: www.agrf.org.au _______________________ Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Yogi Sundaravadanam 2008-05-13T23:23:03 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17957 Hi Jim, I’m looking into it at the moment and been in touch with Paul. I actually require GPR files that have reassigned probes to do my analysis. Cheers Yogi ________________________ Yoganand Sundaravadanam Bioinformatics Officer Australian Genome Research Facility Ltd The Walter and Eliza Hall Institute 1G Royal Pde Parkville VIC 3050 Phone: +61 3 9345 2682 Fax: +61 3 9345 2678 Email: yogi.sundarvadanam-P5e5sBhJi5y6c6uEtOJ/EA< at >public.gmane.org Web: www.agrf.org.au _______________________ Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. -----Original Message----- From: Jim Manos [mailto:jmanos-DVOx7zrZoSe2oFtFVf8vSxCuuivNXqWP< at >public.gmane.org] Sent: Tuesday, May 13, 2008 7:23 PM To: Yogi Sundaravadanam Subject: Hello Yogi, How is the reanalysis coming along? Please let me know as I need to present the data in a seminar on Monday. Best Regards Jim Jim Manos PhD Lecturer in Infectious Diseases, Discipline of Infectious Diseases and Immunology, Blackburn Building University of Sydney [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Yogi Sundaravadanam 2008-05-13T23:16:18 http://comments.gmane.org/gmane.science.biology.informatics.conductor/17951 Dear all, I'm experimenting with machine learning algorithms in microarray domain which require discrete feature space. I'm looking for a paper or any other type of reference dealing with discretization of continuous gene expression data. If somebody is aware on it, please reply to my post. Best regards, Andrej _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Andrej Kastrin 2008-05-13T20:12:22 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.informatics.conductor