I've been wanting to see differential exon usage between two samples and found out about DEXSeq recently. I used the given scripts and generated flattened .GTF file from the .GTF I used to align my reads with TopHat. I generated read numbers from the .SAM files as well.
I am not 100% sure if I'm creating the esc object though. Here's my design d.frame:
and this is the exon count set
after estimating size factors, I call the estimateDispersions function and got this error:
Any ideas what this error might mean?
Thanks!
I am not 100% sure if I'm creating the esc object though. Here's my design d.frame:
Code:
> design condition replicate type cancer.read.counts cancer 1 single-end hesc.read.counts hesc 1 paried-end
Code:
> ECS ExonCountSet (storageMode: environment) assayData: 522962 features, 2 samples element names: counts protocolData: none phenoData sampleNames: cancer.read.counts hesc.read.counts varLabels: sizeFactor condition ... countfiles (5 total) varMetadata: labelDescription featureData featureNames: ENSG00000000003:001 ENSG00000000003:002 ... ENSG00000258375:001 (522962 total) fvarLabels: geneID exonID ... transcripts (13 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation:
Code:
> ECS <- estimateDispersions(ECS, nCores = 12) Estimating Cox-Reid exon dispersion estimates using 12 cores. (Progress report: one dot per 100 genes) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "fData", for signature "NULL"
Thanks!
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