Deseq2 : Paired analysis or otherwise
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6 weeks ago
IM • 0

Dear Community members,

I want to conduct a DESeq2 analysis on 20 samples from 11 donors on a data from a longitudinal study regarding exposure to a certain agent. Each donor has 2 samples except 2 donors (samples discarded due to poor quality). 6 donors have one sample each in both groups of comparison, whereas 3 donors' samples are all in one group. For such an analysis, would a paired analysis be recommended?

design of my analysis

linear-regression paired-analysis DESeq2 longitudinal-analysis • 469 views
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6 weeks ago
ATpoint 82k

Yes, paired analysis is almost certainly your only chance since with human data variance between donors is typically too high to run unpaired analysis at that sample size. You will need to exclude unpaired donors as they don't add for any inference. Of course try unpaired with all samples as well but I doubt it will yield anything substantial.

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Thank you for your reply, ATpoint! Would you recommend that samples from donors 6,8, and 9 also be removed along with unpaired samples of donors 4 and 5?

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In a paired analysis these samples do not add, so maybe remove them.

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