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block design with time course and DESeq2

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

deseq2 time-course block-design
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updated by Ram Ram • written by mccormack • mccormack

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 :

sampleNames <- c("Condition1_timepoint1","Condition2_timepoint1","Condition3_timepoint1","Condition4_timepoint1","Condition1_timepoint2"....)
sampleFiles <- list.files(directory.with.files)
sampleCondition <- c("Condition1","Condition2","Condition3","Condition4","Condition1","Condition2"...)
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updated by Ram Ram • written by tiago211287 tiago211287

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, like Conditon1_timepoint1, Condition2_timepoint1 along with Condition3_timepoint2, Condition4_timepoint2 ? Is there any way I can get results in DESeq2 (or EdgeR) with those 4 specific conditions?

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updated by Ram Ram • written by mccormack • mccormack

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