Differential abundance analysis of two samples with only a single replicate

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4.9 years ago

Ming ▴ 110

Dear All,

I am trying to perform a differential abundance analysis of two sets of samples (Samples A and B), in which they approximately share 20 OTUs.

However, I only have 2 replicates for Sample A, and 1 replicate for sample B.

I will like to find out which OTUs are more quantitatively abundant between the two samples. I have read that DeSeq2 is not possible because I will require replication. Some have recommended R-log transformation.

Are there other ways to go ahead doing this? I was thinking fold-change between the OTU is one method. Will appreciate any feedback or comments.

Thank you!

Deseq2 • 1.2k views

ADD COMMENT • link updated 4.7 years ago by Biostar 20 • written 4.9 years ago by Ming ▴ 110

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In your own mind, is this a statistically valid experimental setup? You could analyse the 2 samples, but what would it mean? Which journal would accept the work for publication?

ADD REPLY • link 4.9 years ago by Kevin Blighe 87k

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