I am using HTseq pipeline for DESeq2:
Directory = "/Users/abhaykanodia/Desktop/smallRNA/"
condition = c("WT1", "WT2", "WT3",
"NTC1", "NTC2", "NTC3")
sampleFiles= c("AK1a_counts.txt","AK2a_counts.txt","AK3a_counts.txt","
AK4a_counts.txt","AK5a_counts.txt","AK6a_counts.txt")
sampleName = c("AK1", "AK2", "AK3", "AK4", "AK5", "AK6")
sampleTable <- data.frame(sampleName = sampleName, fileName = sampleFiles, condition = condition)
sampleTable
The output is:
sampleName fileName condition 1 AK1 AK1a_counts.txt WT1 2 AK2 AK2a_counts.txt WT2 3 AK3 AK3a_counts.txt WT3 4 AK4 AK4a_counts.txt NTC1 5 AK5 AK5a_counts.txt NTC2 6 AK6 AK6a_counts.txt NTC3``` Now, when I use:
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
directory = Directory,
design= ~ condition)
It gives the following error:
Error in colnames<-(*tmp*, value = sampleTable[, 1]) :
attempt to set 'colnames' on an object with less than two dimensions
