Dear Alejandro, Thank you for your reply, sorry for the delayed response I have been away. This is the output: > gns <- as.character(goi$Gene.ID) > all( gns %in% levels( geneIDs( ecs ) ) ) [1] FALSE > gns %in% levels( geneIDs( ecs ) ) [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE [13] TRUE TRUE TRUE TRUE TRUE TRUE Now when I check them individually, it appears that the 2 are in combination with another gene respectively: fData(ecs)$geneID[grep(goi$Gene.ID[11],fData(ecs)$geneID)] [1] ENSG00000267002+ENSG00000012048 ENSG00000267002+ENSG00000012048 [3] ENSG00000267002+ENSG00000012048 ENSG00000267002+ENSG00000012048 [5] ENSG00000267002+ENSG00000012048 ENSG00000267002+ENSG00000012048 ..... (73x) > fData(ecs)$geneID[grep(goi$Gene.ID[12],fData(ecs)$geneID)] [1] ENSG00000256664+ENSG00000135679 ENSG00000256664+ENSG00000135679 [3] ENSG00000256664+ENSG00000135679 ENSG00000256664+ENSG00000135679 [5] ENSG00000256664+ENSG00000135679 ENSG00000256664+ENSG00000135679 .... (62x) BW, Natasha -----Original Message----- From: Alejandro Reyes [mailto:alejandro.reyes@embl.de] Sent: 25 March 2013 08:29 To: Natasha Sahgal Cc: bioconductor at r-project.org Subject: Re: [BioC] DEXSeq html report error Dear Natasha, Thanks for your report. Sounds strange, just to make sure. What is the result of the code below? gns <- as.character(goi$Gene.ID) all( gns %in% levels( geneIDs( ecs ) ) ) Bests, Alejandro > Dear List, > > I am trying to generate an html report for my DEXSeq output, but only for certain genes of interest. > I keep getting an error that I do not understand! > ======== > Code: >> ecs > ExonCountSet (storageMode: environment) > assayData: 622936 features, 3 samples > element names: counts > protocolData: none > phenoData > sampleNames: 230 231 232 > varLabels: sizeFactor Name ... countfiles (9 total) > varMetadata: labelDescription > featureData > featureNames: ENSG00000000003:E001 ENSG00000000003:E002 ... > ENSG00000267801:E001 (622936 total) > fvarLabels: geneID exonID ... log2fold(Mut/Cont) (14 total) > fvarMetadata: labelDescription > experimentData: use 'experimentData(object)' > Annotation: > >> head(goi) > Genes Gene.ID Chrom > 1 ABCB7 ENSG00000131269 X > 2 FTMT ENSG00000181867 5 > 3 ALAS2 ENSG00000158578 X > 4 TP53 ENSG00000141510 17 > 5 P21 (CDKN1A) ENSG00000124762 6 > 6 PUMA (BBC3) ENSG00000105327 19 > >> dim(goi) > 18 3 > >> DEXSeqHTML(ecs,geneIDs=goi$Gene.ID,color=c("red","blue"),file="goi_MC >> .html") > Error in DEXSeqHTML(ecs, geneIDs = goi$Gene.ID, color = c("red", "blue"), : > The geneIDs provided are not in the ecs object > >> DEXSeqHTML(ecs,geneIDs=goi$Gene.ID,color=c("red","blue"),file="goi_MC >> .html",FDR=1) > Error in DEXSeqHTML(ecs, geneIDs = goi$Gene.ID, color = c("red", "blue"), : > The geneIDs provided are not in the ecs object ======== > > I can't figure out what the problem is? To me it appears that all the > ids in the goi object are present in the ecs object > >> grep(goi$Gene.ID[1],fData(ecs)$geneID) > Any help much appreciated. > > > Many Thanks, > Natasha > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] WriteXLS_2.3.0 gdata_2.12.0 DEXSeq_1.4.0 Biobase_2.18.0 > [5] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 gtools_2.7.0 hwriter_1.3 plyr_1.7.1 RCurl_1.95-3 > [6] statmod_1.4.16 stringr_0.6.1 tools_2.15.2 XML_3.95-0.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor