RPKM/CPM/FPKM to log2 units · Biostar

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RPKM/CPM/FPKM to log2 units

Hi,

In network analysis on RNA seq data. Should the RPKM/CPM/FPKM be converted to log2 units?

Regards

rpkm log2

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updated 6.6 years ago by dsull

• written 6.6 years ago by zhang.jianhai •

1 answer

What type of network analysis are you doing?

In general, it's best to use counts normalized in DESeq2 via the varianceStabilizingTransformation function.

For example, if you're doing WGCNA, the FAQ suggests the following:

"We then recommend a variance-stabilizing transformation. For example, package DESeq2 implements the function varianceStabilizingTransformation which we have found useful, but one could also start with normalized counts (or RPKM/FPKM data) and log-transform them using log2(x+1). For highly expressed features, the differences between full variance stabilization and a simple log transformation are small." - https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html

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written 6.6 years ago by dsull

I am doing gene co-expression network analysis on RNA-seq data. The only expression matrix I received is RPKM/FPKM/CPM, so I am wondering if it should be further log2 transformed?

Regards.

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written 6.6 years ago by zhang.jianhai •

If you're going to use FPKM, then yes, you should log2-transform (which is exactly what the FAQ above states so just go off of that).

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written 6.6 years ago by dsull

Got it. Thank you so much!

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written 6.6 years ago by zhang.jianhai •

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