DESeq2-No replicates-Utility of log2fold shrunk values?
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bn3301 • 0
@bn3301-15048
Last seen 5.2 years ago

I am using DESeq2 to estimate fold changes between two conditions neither of which have any replicates.

Will it be of any utility to use log2fold shrunken changes over the non-shrunken ones in this case?

deseq2 rnaseq • 597 views
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@mikelove
Last seen 1 hour ago
United States

For no replicate experiments, I'd suggest applying the vst() and then you can just calculate the simple difference between the two samples. This will give you a log2 fold change that is moderated, such that small counts do not produce large LFC (avoiding having to pick a pseudocount).

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