I know I can filter my counts matrix using this command
filtered.counts <- counts[rowSums(counts==0)<3, ]
when I would like to keep genes with counts in more than three samples.
But is there a way to do the same and removes rows from the matrix when this three
0 are in only one condition?
I have 2 conditions with each four replica. I would like to filter for genes with counts in at least two of them.
Would this kind of filtering make sense? Or do I create a bias in the expression matrix?