How to plot PCA with fpkm values

Hello All

I have file containing 8 columns

column  1 gene_id
column 2 gene_short_name
column 3 FPKMcontrol1
column 4 FPKMcontrol2
column 5 FPKMcontrol3
column 6 FPKMtest1
column 7 FPKMtest2
column 8 FPKMtest3

This is human samples with 22632 genes
I want plot PCA using this samples
How to go about I am new to PCA analysis
i want to draw pca using fpkm
Any help
Thank you

pca plot rnaseq fpkm

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updated 8.6 years ago by Ram

• written 9.5 years ago by raya.girish •

2 answers

Check this previous post: PCA plot of RPKM data from RNA-Seq dataset

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written 9.5 years ago by igor

You should convert FPKM into log plus one TPM. To convert FPKM into TPM, simply divide each FPKM value by its sample sum; then multiply it by a million.

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written 9.5 years ago by shunyip

Why should FPKM be converted to TPM? Why is this a requirement?

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written 9.3 years ago by fr

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