DEXSeq error:Failed to set up model frames for genes

[zhuya5607]

Here is how I produced the error:
annotationfile=file.path(inDir,"Homo_sapiens.GRCh37.68.DEXSeq.chr.gff")
esc=read.HTSeqCounts(countfiles=file.path(inDir,paste(rownames(samples),"txt",sep=".")),design=samples,flattenedfile=annotationfile)
sampleNames(esc)=rownames(samples)
esc<- estimateSizeFactors(esc)
design(esc)
condition libType
H0-R1exoncount H0 paired-end
H0-R2exoncount H0 paired-end
H0-R3exoncount H0 paired-end
H24-R1exoncount H24 paired-end
H24-R2exoncount H24 paired-end
H24-R3exoncount H24 paired-end

esc<- estimateDispersions(esc)

Everything is working fine until the estimateDispersions step, I got the following warning messages:
1: In .local(object, ...) :
Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
2: In .local(object, ...) :
Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon
3: In .local(object, ...) :
Failed to set up model frames for genes ENSG00000000003, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000001036, ENSG00000001084+ENSG00000231683, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001617, ENSG00000001629, ENSG00000001630+ENSG00000240720, ENSG00000001631+ENSG00000243107, ENSG00000002079, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000003056, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003987, ENSG00000004059+ENSG00000106328, ENSG00000004399, ENSG00000004455, ENSG00000004478, ENSG00000004487, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004777, ENSG00000004779, ENSG00000004838, ENSG00000004864, ENSG00000004897, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG0000000 [... truncated]

Does anyone know what is the problem?


sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

other attached packages:
[1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0

[dpryan]

I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).

[zhuya5607]

I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).

Thanks, I will try it.

[zhuya5607]

I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).

I updated DEXSeq to 1.2.1, but it still gives exactly same warning message.

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

other attached packages:
[1] DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.1 DBI_0.2-5 DESeq_1.8.3
[4] IRanges_1.14.4 RColorBrewer_1.0-5 RCurl_1.91-1
[7] RSQLite_0.11.1 XML_3.9-4 annotate_1.34.1
[10] biomaRt_2.12.0 genefilter_1.38.0 geneplotter_1.34.0
[13] grid_2.15.1 hwriter_1.3 plyr_1.7.1
[16] splines_2.15.1 statmod_1.4.15 stats4_2.15.1
[19] stringr_0.6.1 survival_2.36-14 tools_2.15.1
[22] xtable_1.7-0

[dpryan]

I updated DEXSeq to 1.2.1, but it still gives exactly same warning message.

Hmm, in that case I don't know. I was able to track down the error by going through the code for estimateDispersions (I think), which threw an error when trying to call glmnb.fit or something like that. I think the version I had was incorrectly calling the function or something like that. You might give something like that a try or just shoot an email to one of the package maintainers.

[areyes]

Hi zhuya5607,

As dpryan pointed out, I have corrected this in DEXSeq 1.2.1. It is strange that it is giving you troubles also this last version and actually I can not reproduce this error! Would you mind sending me your ExonCountSet object with a reproducible code? so I could take a closer look?

Alejandro

[zhuya5607]

Hi zhuya5607,

As dpryan pointed out, I have corrected this in DEXSeq 1.2.1. It is strange that it is giving you troubles also this last version and actually I can not reproduce this error! Would you mind sending me your ExonCountSet object with a reproducible code? so I could take a closer look?

Alejandro

Hi, Alejandro

I found out why I still got the same error when I updated to DEXSeq 1.2.1. Because I was using R-studio, a Graphical interface tool, which saves the workplace when I log out. So, when I log in to R again after update, it actually loaded the saved workplace in which the old version DEXSeq 1.20 is attached.
But the weird thing is that the sessionInfo() shows I was using the new version.

There is no error now when I reload the new version.

Thanks for your and dpryan's kind help!