Microarray Data Analysis using DEseq2

Question

[shashank.jatav]

Hey All,

Can one analyze affymetrix microarray data with Deseq2? I know that Deseq2 can only analyze count data but can I tweak microarray data to use it with DEseq2 (like combining perfect matching probes expression values and using it). Would it be recommended considering algorithm differences between limma and deseq2?

Answer 1

[WouterDeCoster]

DESeq2 is meant for count data, and since the distribution of counts and intensities is quite different it should not be applied to microarray data. I think using limma for microarray data is perfectly fine and there is no need to use DESeq2.