I have a project on Rice and my conditions (paired-end) unfortunately have no replicate.
I used tophat2 and after conversion to sam file is used HTSeq and I merged HTSeq output.
And today the bigest problem emereged, How can i handle DeSeq without replicate you can see my following codes:
pasillaCountTable <- read.table("MyCountTable.txt") pasillaDesign = data.frame(row.names = colnames( pasillaCountTable ),condition = c( "C1","S1"),libType = c( "paired-end", "paired-end" )) pairedSamples = pasillaDesign$libType == "paired-end" countTable = pasillaCountTable[ , pairedSamples ] condition = pasillaDesign$condition[ pairedSamples ] cds = newCountDataSet( countTable, condition ) cds = estimateSizeFactors( cds )
and main part was, is it fine or not?
cds = estimateDispersions( cds, method="blind", sharingMode="fit-only" ,fitType="local")
and rest of the codes:
res_C1S1 = nbinomTest( cds, "C1", "S1" ) write.table(res_C1S1,"C1_S1.txt",sep= "\t")