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owkin / PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
https://pydeseq2.readthedocs.io/en/latest/
MIT License
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How to process gene expression data from Affymetrix in Python #270

Closed abearab closed 4 months ago

abearab commented 4 months ago

I'm trying to perform some basic DE analysis on https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171053. How could I do that with pyDESeq2?

I saw this in biostars from 5 years and hopefully now the answer is pyDESeq2!

Don't do that in python. Use established R packages to analyse microarrays. See this tutorial.

vcabeli commented 4 months ago

Hello @abearab, unfortunately pyDESeq2 is not compatible with affymetrix data, since the DESeq2 algorithm is designed for count data with a particular distribution.

I would use limma in R, or you could try looking for a maintained python implementation of limma but I'm not sure that exists

abearab commented 4 months ago

Hello @abearab, unfortunately pyDESeq2 is not compatible with affymetrix data, since the DESeq2 algorithm is designed for count data with a particular distribution.

I would use limma in R, or you could try looking for a maintained python implementation of limma but I'm not sure that exists

Hello,

Thanks for your reply. That makes sense, I'm going to use limma then.