Question: MaSigPro - pre-filtering of genes
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gravatar for GFM
3.6 years ago by
GFM20
European Union
GFM20 wrote:

Hello,

I have a question regarding pre-filtering of genes in RNA-Seq data for MaSigPro.

I have filtered out genes that the counts in all samples was low. In some data sets I did not get significant genes. I thought to further filter the data, to keep only genes had a difference above of 1.5 between any 2 samples:
keep only genes with: (max (counts in all samples)/min(counts in all samples) > 1.5

I then managed to get significant genes.
I wanted to ask whether it is a good workflow to have that per-filtering? And if so, would you suggest to do it always, or only in cases that no significant genes are obtained.

Thanks.
 

masigpro • 487 views
ADD COMMENTlink written 3.6 years ago by GFM20
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