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
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
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