Question: different designs for finding DEG by limma
gravatar for amin.ghareyazi
10 weeks ago by
amin.ghareyazi0 wrote:


I have a normalized and batch effect removed microarray data. I have 5 groups of samples namely S1 to S5. I have to find differentially expressed genes in 3 conditions below:

1) one group vs remaining groups (for example S2 VS S1,S3,S4,S5)

2) differentially expressed genes across all 5 groups

3) all comparisons between 2 groups.

I just wanted to know how should I define my questions in model.matrix() and makeContrasts() functions to analyze my data.

limma design deg • 103 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by amin.ghareyazi0

Are you sure you want to do THAT many comparisons? Could you elaborate on what are those 'groups' actually correspond to? How was your MDS plot? Do you see any clustering of the samples?

I can't imagine the number of pairwise comparisons if you want to do your contrast No. 3 (Well, I actually can. That's a LOT for sure).

ADD REPLYlink written 10 weeks ago by mikhael.manurung200

Groups in samples are from 5 types of cancer. I didn't find any use for MDS plots. And you are right about number of pairwise comparisons. Actually I am more interested in finding DEG for No. 1 and 2. Third one will be used for some rare situations in my study. Can you help me at least for No. 1 and 2? I would appreciate your help.

ADD REPLYlink written 10 weeks ago by amin.ghareyazi0
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