[BioC] DEXSeq html report error

[Natasha Sahgal]

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 at 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
>
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