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Microarray Data Analysis using DEseq2

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?

deseq microarray
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updated by WouterDeCoster WouterDeCoster • written by shashank.jatav • shashank.jatav

1 answer

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.

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written by WouterDeCoster WouterDeCoster

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