Hi,
I have a number of RNA-Seq samples (476 in total) classified into three groups "1", "2" and "3".
Following the new workflow (cuffquant) I have provided cuffdiff with a sample sheet and have received the results of the three contrasts "1vs2", "1vs3" and "2vs3". So far so good...
But now I would like to test "1vs2+3", "2vs1+3" and "3vs1+2" - so each group in contrast to the other two.
Can I do this using a contrast file? The example in the manual does not suggest this...
Or do I have to provide three new samplesheets with two groups in each (e.g. "1" and "2+3" for one of the paired contrasts)?
Thanks,
Jakob
I have a number of RNA-Seq samples (476 in total) classified into three groups "1", "2" and "3".
Following the new workflow (cuffquant) I have provided cuffdiff with a sample sheet and have received the results of the three contrasts "1vs2", "1vs3" and "2vs3". So far so good...
But now I would like to test "1vs2+3", "2vs1+3" and "3vs1+2" - so each group in contrast to the other two.
Can I do this using a contrast file? The example in the manual does not suggest this...
Or do I have to provide three new samplesheets with two groups in each (e.g. "1" and "2+3" for one of the paired contrasts)?
Thanks,
Jakob
