DEXSeq - creating new ExonCountSet from scratch

[ahmetz]

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:

> design
                   condition replicate       type 
cancer.read.counts    cancer         1 single-end
hesc.read.counts        hesc         1 paried-end

and this is the exon count set

> 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:

after estimating size factors, I call the estimateDispersions function and got this error:

> 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"

Any ideas what this error might mean?

Thanks!

[Simon Anders]

I'm not sure why the error message is not more informative, but the the reason is probably that you do not have any replicates and hence, a statistical analysis is not possible.