How to perform PCA analysis
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
• 2,821 views
•
link
updated
by
Kevin Blighe
•
written
by
francesca3 •
•
written
by
francesca3 •
1 answer
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
• 0 views
•
link
written
by
Kevin Blighe
Log in to answer this question.
More posts like this
-
pre-proccessing of RNAseq data for WGCNA
written by txtbookir •
-
How to convert log2 scale RNA-Seq expression data to linear scale data
written by mohammedtoufiq91
-
Correlation analyses on TCGA data
written by mario.keller.1988 •
-
CPM function in EDGER
written by francesca3 •
-
CPM or TPM in GSEA analysis
written by francesca3 •
-
CPM or TPM in GSEA analysis
written by francesca3 •
-
Input data in GAGE Analysis
written by francesca3 •
-
How to filter low expressed genes based on TPM expression?
written by newbie
-
How to convert log2FC (Fold Change) obtained by differential expression analysis by DESeq2 to FC
written by sole.r.v •
-
scRNA-seq, filter low expressed genes based on RPKM value
written by chipolino •
Follow @Kevin's guides in:
PCA plot from read count matrix from RNA-Seq
PCA in a RNA seq analysis