Entering edit mode
8.6 years ago
mccormack
▴
90
I have four conditions: wt, mut, wt-treat, mut-treat
where each of the 4 conditions have 8 time points (in duplicate), so 32 conditions, 64 samples
I would like to use DESeq2 with all the samples (create a dds object with all 64 samples), but be able to test for wt-0timept, mut-0timept, wt-treat-4hr, mut-treat-4hr in a block design. So, there are two different time points being tested.
I think I would know how to do this for a single time point, but I can not figure out how to do it when two time points (and 4 conditions, wt, mut, treat, no-treat) are in the comparison. Is this possible ?
Matthew
If I would have to do this, I think I would treat each condition time point as a group, and put all together in a single big deseq run.
Because Deseq2 will compare each sample with any other sample anyway. You could make a big heatmap and PCA plot to see your sample behavior. And use contrast to see the relation of One sample to Other Sample.
So in the
sampleTable
data.frame I would do :Hi tiago211287,
Thank you very much for your reply.
If I get my results with contrast and use condition and use something like
condition = c('contrast', 'Condition1', 'Condition4')
, then I will be calling on all the time points for Condition1 and Condition4. But, what if I just want specific time points, likeConditon1_timepoint1
,Condition2_timepoint1
along withCondition3_timepoint2
,Condition4_timepoint2
? Is there any way I can get results in DESeq2 (or EdgeR) with those 4 specific conditions?