Can I conduct PCA using FPKM data from RNAseq?

12 August 2022 1 6K Report

I only get a set of FPKM data of several different cancer cell lines from an RNAseq experiment. Now I want to conduct PCA and other clustering methods. Heard that those methods prefer a DESeq results to be the input, what will be the difference if I use FPKM to calculate the PCs?

And is there an alternative method?

Shafagat Mahmudova

Dear Lu Qiu ,

Look the link, maybe useful.

https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/43389-interpretation-of-pca-of-fpkm-values

Regards,

Shafagat

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