Hi all,
I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with diffData(). I have restricted significance results to one pairwise comparison with getSig (). This works great. However, when I try to do the same with getDiff() comparisons between all samples are reported. I have included the code below. Any thoughts on why this does not work?
Thank you in advance for the help.
I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with diffData(). I have restricted significance results to one pairwise comparison with getSig (). This works great. However, when I try to do the same with getDiff() comparisons between all samples are reported. I have included the code below. Any thoughts on why this does not work?
Code:
... diffGenesIds<-getSig(cuff,x='B73',y='B74',alpha=0.05,level='genes') diffGenes<-getGenes(cuff,diffGenesIds) names<-featureNames(diffGenes) row.names(names)=names$tracking_id diffGenesNames<-as.matrix(names) diffGenesNames diffGenesNames<-diffGenesNames[,-1] diffGenesNames diffGenesData<-diffData(diffGenes,x='B73',y='B74') row.names(diffGenesData)=diffGenesData$gene_id diffGenesData<-diffGenesData[,-1] diffGenesData ...
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