Hey,
I'm trying to prepare my Tophat accepted hits bam files for DESeq.
However, as always there seems to be a glitch in my script that I can't figure out:
> setwd ('/home/sylvia')
> library(easyRNASeq)
> library('biomaRt')
> library(BSgenome.Hsapiens.UCSC.hg19)
SerumRNAseq.count <- easyRNASeq(filenames=c('TQ24_tophat_accepted_hits_sorted_paired.bam','TQ25_accepted_hits_sorted_paired.bam','TQ28_accepted_hits_sorted_paired.bam','TQ29_sorted_paired.bam'), organism='Hsapiens', count='genes', annotationMethod='biomaRt', outputFormat='DESeq', readLength=100L)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function âeasyRNASeqâ for signature â"missing"â
I tried changing annotationMethod to rda (though I don't have the file yet), outputFormat to RNAseq, count to exons, I even loaded the chr.sizes manually although they should get extracted from the bam header - no change, the error message stays the same.
I just can't figure out what signature "missing" is supposed to stand for!?!
Any help much appreciated
I'm trying to prepare my Tophat accepted hits bam files for DESeq.
However, as always there seems to be a glitch in my script that I can't figure out:
> setwd ('/home/sylvia')
> library(easyRNASeq)
> library('biomaRt')
> library(BSgenome.Hsapiens.UCSC.hg19)
SerumRNAseq.count <- easyRNASeq(filenames=c('TQ24_tophat_accepted_hits_sorted_paired.bam','TQ25_accepted_hits_sorted_paired.bam','TQ28_accepted_hits_sorted_paired.bam','TQ29_sorted_paired.bam'), organism='Hsapiens', count='genes', annotationMethod='biomaRt', outputFormat='DESeq', readLength=100L)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function âeasyRNASeqâ for signature â"missing"â
I tried changing annotationMethod to rda (though I don't have the file yet), outputFormat to RNAseq, count to exons, I even loaded the chr.sizes manually although they should get extracted from the bam header - no change, the error message stays the same.
I just can't figure out what signature "missing" is supposed to stand for!?!
Any help much appreciated