This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DESeq2 for DE analysis of proteins

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!

proteomics deseq2
• 2,140 views • link
updated by dsull dsull • written by 4732b159 • 4732b159

1 answer

What do your protein values look like? If they are intensity values rather than whole number values, why not use limma as many people do?

DESeq2 depends on whole number counts being negative binomially distributed.

• 0 views • link
written by dsull dsull

Thanks for your response, could you please elaborate what you mean?

• 0 views • link
written by 4732b159 • 4732b159

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.

• 0 views • link
written by dsull dsull

Oh I see what you mean now, yes my data consists of whole numbers as expression counts.

• 0 views • link
written by 4732b159 • 4732b159

DESeq2 requires the data being expressed according to a binomial negative.

• 0 views • link
written by Antonio R. Franco Antonio R. Franco

Correct, and if it's whole numbers, check if it obeys that distribution; e.g. make a mean vs. variance plot.

• 0 views • link
written by dsull dsull

Log in to answer this question.

More posts like this