[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!
> ecs
ExonCountSet (storageMode: environment)
assayData: 622936 features, 3 samples 
  element names: counts 
protocolData: none
  sampleNames: 230 231 232
  varLabels: sizeFactor Name ... countfiles (9 total)
  varMetadata: labelDescription
  featureNames: ENSG00000000003:E001 ENSG00000000003:E002 ...
    ENSG00000267801:E001 (622936 total)
  fvarLabels: geneID exonID ... log2fold(Mut/Cont) (14 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

> 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,

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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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