I'm having some trouble getting running DEXSeq. I generated count files using the python scripts and have gotten as far as trying to fit the dispersion function, which fails with an error:
I'm guessing the error (about missing values) is probably a result of the NaNs produced. estimateDispersions didn't give any warnings or errors. To be honest, I'm not even sure where the NaNs are coming from -- I'm guessing it's not a problem that there are exons with a zero count, right? I'm at a loss about what to try next, so I would be very grateful for a pointer in the right direction (or maybe even a solution). If some extra information would be helpful in sorting this out, please let me know.
Thanks!
> a186Exons
ExonCountSet (storageMode: environment)
assayData: 170526 features, 4 samples
element names: counts
protocolData: none
phenoData
sampleNames: wt-1 wt-2 a186-3 a186-4
varLabels: sizeFactor condition ... countfiles (5 total)
varMetadata: labelDescription
featureData
featureNames: AT1G01010:001 AT1G01010:002 ... ATMG01410:001 (170526 total)
fvarLabels: geneID exonID ... transcripts (13 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> pData(a186Exons)
sizeFactor condition replicate type countfiles
wt-1 1.9951460 W 1 paired-end wt-1
wt-2 1.2640540 W 2 paired-end wt-2
a186-3 0.8502673 m 1 paired-end a186-3
a186-4 0.5048640 m 2 paired-end a186-4
> a186Exons=fitDispersionFunction(a186Exons)
Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break :
missing value where TRUE/FALSE needed
In addition: Warning message:
In log(coefs/oldcoefs) : NaNs produced
ExonCountSet (storageMode: environment)
assayData: 170526 features, 4 samples
element names: counts
protocolData: none
phenoData
sampleNames: wt-1 wt-2 a186-3 a186-4
varLabels: sizeFactor condition ... countfiles (5 total)
varMetadata: labelDescription
featureData
featureNames: AT1G01010:001 AT1G01010:002 ... ATMG01410:001 (170526 total)
fvarLabels: geneID exonID ... transcripts (13 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> pData(a186Exons)
sizeFactor condition replicate type countfiles
wt-1 1.9951460 W 1 paired-end wt-1
wt-2 1.2640540 W 2 paired-end wt-2
a186-3 0.8502673 m 1 paired-end a186-3
a186-4 0.5048640 m 2 paired-end a186-4
> a186Exons=fitDispersionFunction(a186Exons)
Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break :
missing value where TRUE/FALSE needed
In addition: Warning message:
In log(coefs/oldcoefs) : NaNs produced
Thanks!
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