Question

DESeq2 with 2 biological replicates: if the replicates are not compatible for some genes

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f_rahmdani • 0

@f_rahmdani-23913

Last seen 16 hours ago

Canada

I did DE analysis on 80 libraries with DESeq2, the number of biological replicates is 2 (40 samples). For some genes, there is a big difference between read counts for 2 replicates, for example r1:2 and r2:2436. If the number of replicates was more than 2, these cases were removed as an outlier. How to solve it with 2 biological replicates? Thanks

deseq2 • 1.3k views

ADD COMMENT • link updated 4.4 years ago by Michael Love 43k • written 4.4 years ago by f_rahmdani • 0

score 2 · Answer 1 · 2020-07-27

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Michael Love 43k

@mikelove

Last seen 6 days ago

United States

There is no great answer that statistical methods can provide here.

This reason is exactly what I say to people who propose to perform n=2 experiments: "What will you do if the two replicates are in total disagreement? How will you know if either or both experiments had a technical issue?"

ADD COMMENT • link 4.4 years ago Michael Love 43k

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Thanks a lot Michael for the quick response! You are absolutely right; but is there any way to eliminate both replicates in these cases?

ADD REPLY • link 4.4 years ago f_rahmdani • 0

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I don’t have any recommendations other than using QC metrics per sample, eg MultiQC