Question: Is it possible to run DESeq with only two replicates in one group?
0
gravatar for  DataFanatic
4 weeks ago by
DataFanatic230
DataFanatic230 wrote:

Is it possible to run DESeq with only two replicates in one group? I have treatment n=3 and control n=2 Can I still ran DESeq2, if it is not possible can you recommend other packages, please?

rna-seq deseq2 replicates • 104 views
ADD COMMENTlink modified 4 weeks ago by ATpoint36k • written 4 weeks ago by DataFanatic230
2

You can run DESeq2, edgeR, limma::voom, and others. The problem is your experiment you be under-powered - a minimum number of replicates to get good statistical power is 5-6 samples.

ADD REPLYlink written 4 weeks ago by h.mon30k
2
gravatar for ATpoint
4 weeks ago by
ATpoint36k
Germany
ATpoint36k wrote:

This is perfectly fine. h.mon is right that more replicates are desirable and beneficial to make results more robust but n=2 and n=3 are common replicate numbers and the standard tools including DESeq2 are well-able to derive proper statistics from low replicate numbers.

ADD COMMENTlink written 4 weeks ago by ATpoint36k
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