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9 weeks ago
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Hello, Does anyone use DESeq2 for differential expression of "proteins" (data is an expression count matrix of proteins), and have suggestions on whether suitability/limitations of the package etc.? Thanks!
Thanks for your response, could you please elaborate what you mean?
If your protein "counts" look like:
Protein A: 0.4 Protein B: 4.583 Protein C: 3.582 Protein D: 2.492
Then you CAN'T use DESeq2 (see the decimals; they aren't whole numbers, they are CONTINUOUS numbers).
Just use the limma package for your DE analysis.
Oh I see what you mean now, yes my data consists of whole numbers as expression counts.
DESeq2 requires the data being expressed according to a binomial negative.
Correct, and if it's whole numbers, check if it obeys that distribution; e.g. make a mean vs. variance plot.