How am I supposed to perform differential expression with .cel files ?

Question

[Bhanu]

I want to perform differential analysis on GSE90603_RAW which contains miRNA microarray data, but I'm not sure how it's done with .cel files

[Hyper_Odin]

You can use R to read it http://www.sthda.com/english/wiki/affymetrix-cel-files

[Bhanu]

Thanks but what am I supposed to do after normalization?

Answer 1

[Matthias Zepper]

The platform of your array is GPL21572, so after normalization, your measured probe set intensities are proportional to the miRNA quantities in your sample. Subsequently, you can perform differential microarray expression like you would do that for genes. Also mind that there are dedicated miRNA packages for in-depth analysis.