Use of RSEM counts in WGCNA
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harelarik ▴ 50
@harelarik-13564
Last seen 9 months ago

What is the procedure to use RSEM counts in WGCNA? Can one use normalized (e.g., lcpm+prior 0.25 ) RSEM for input in WGCNA? Does one need round the RSEM counts ?

Thank you,

Arik

rsemmed RSEM WGCNA • 303 views
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@kevin
Last seen 12 hours ago
Republic of Ireland

WGCNA is not a Bioconductor package, but it's okay generally to post here.

The answer is that, yes, you can use RSEM, and, no, you should not have to round these values.

See this quote:

Yes. As far as WGCNA is concerned, working with (properly normalized) RNA-seq data isn't really any different from working with (properly normalized) microarray data.

Further:

Whether one uses RPKM, FPKM, or simply normalized counts doesn't make a whole lot of difference for WGCNA analysis as long as all samples were processed the same way.

Source: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html

Kevin

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Thank you Kevin. The issue with RSEM is that the data contains many values between 0 and 1, after (log+prior) normalization they become approximately zero. However, genes with many zero samples should be filtered out.

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