[BioC] DEXSeq html report error
Natasha Sahgal
nsahgal at well.ox.ac.uk
Sat Mar 23 01:04:37 CET 2013
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
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