exonmap error & questions (Affy mouse exon arrays)
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@wolfgang-raffelsberger-1805
Last seen 8.4 years ago
Dear Bioconductors, I have a few questions concerning the use of the exonmap package for (mouse) Affymetrix exon arrays : Following the instructions from the exonmap-vignette or the "example workflow" one typically first creates a vector called 'sigs' containing the retained/selected (row)names of rma-processed probe-sets. If I understand right, the exonmap package uses identifiers different to the ones from Affymetrix. In the case of my mouse data I get for sigs something like "4304922","4304923" etc. Following the "example workflow" unfortunately I can't get the select.probewise() function working (see code below). Besides, I have difficulty in aligning the results of exon.details() to the original data (see code below). When using other methods (than pc() ) for identifying differentially expressed genes I get stuck at the step of adding/showing my test-statistics or original data together with the results from exon.details() or gene.details() . Last point : Is there a way to retreive the corresponding Affymetrix IDs ? (I guess the QSL tables contain this information: Could this be it the table "probeset" ?) Thanks inadvance for all hints, Wolfgang Here the code : library(exonmap) ; library(affy) xmapDatabase("Mouse") dat.raw <- read.exon() dat.raw at cdfName <- "mouseexonpmcdf" eset.rma <- rma(dat.raw) pc.rma <- pc(eset.rma,"treatment",c("wt","KO")) sigs <- names(fc(pc.rma))[abs(fc(pc.rma)) > 1 & tt(pc.rma) < 1e-04] sigs[1:2] # get: "4304922","4304923" , ... # problem with filtering : sigs.exonic <- select.probewise(sigs,filter="exonic") # mt.level : multi-target score to filter by # get : Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: Column 'probeset_id' in field list is ambiguous) # similarly with the command below I get the same error as above .. sigs.intronic <- select.probewise(sigs,filter=c("intronic")) # mt.level : multi-target score to filter by # get : Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: Column 'probeset_id' in field list is ambiguous) ## now suppose that I selected exons by another method than pc() and that they are in sigs1 sigs1[1:2] # get : "4304925","4304927", ... # similarly I run sig1.exons <- probeset.to.exon(sigs1) sig1.genes <- probeset.to.gene(sigs1) sig1.transcr <- probeset.to.transcript(sigs1) # probeset.details(sig.exons) gene.details(sig1.genes) # OK exon.details(sig1.exons) # OK # the functions used above gives a very nice summary about the gene & exon infomation; # but how can I find out which elements of my initial data they represent ? {ie map it to rownames(exps(eset.rma)) } # I would need this if I wanted to show for example my alternative test-statstics or the the intial RMA values as an additonal column ... > sessionInfo() R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] limma_2.14.4 exonmap_1.6.02 plier_1.10.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.14.05 gcrma_2.12.1 matchprobes_1.12.0 [10] genefilter_1.20.0 survival_2.34-1 affy_1.16.0 [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.0.6 RSQLite_0.6-8 annotate_1.18.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 http://www-bio3d-igbmc.u-strasbg.fr/~wraff wolfgang.raffelsberger at igbmc.fr
exonmap exonmap • 747 views
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