Question

How to perform PCA analysis

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4.2 years ago

francesca3 ▴ 140

Hi everyone, I have the edge results with all the values (logFC, FC, logCPM, CPM, RPKM, TPM). Which values should I use perform the PCA? Second question: which values should I use to filter out the genes with a low expression before performing it? Cpm or RPKM?

Thanks

RNA-Seq PCA • 1.8k views

ADD COMMENT • link updated 4.2 years ago by Kevin Blighe 87k • written 4.2 years ago by francesca3 ▴ 140

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Follow @Kevin's guides in:
PCA plot from read count matrix from RNA-Seq
PCA in a RNA seq analysis

ADD REPLY • link 4.2 years ago by GenoMax 141k

score 2 · Answer 1 · 2020-01-30

Hello, please use logCPM, as the distribution of these is more 'amenable' to transformation via PCA.

For filtering, there is no standard. You could go by RPKM < 10 (for not expressed). Others will have other opinions.

Obviously, I also recommend that you use my own package: https://bioconductor.org/packages/release/bioc/html/PCAtools.html

Kevin