Question: Can I calculate the effect size from log2FoldChange in gene expression?
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gravatar for ev97
11 days ago by
ev970
ev970 wrote:

Hello, I am new here. I am trying to solve my problem and I do not know if someone has asked this before. I searched about it, but I couldn't find something similar. If it is the case, I am sorry if I am asking you the same thing.

Just in case, can someone help me?

I have used DEseq2 tool for estimate gene expression and I want to rank the significant genes using another method to estimate the effect size. In order to estimate this effect, I want to calculate Hedge's g and Cohen's d. I know that there is a package named "effsize" which has both type of effect sizes.

https://www.rdocumentation.org/packages/effsize/versions/0.8.1/topics/cohen.d

However, I don't know how to use that function (cohen.d) with the DEseq2 results.

Do you know if it is possible to use log2foldchange values (from my DEseq2 results?

Thanks very much in advance

Regards

ADD COMMENTlink modified 11 days ago • written 11 days ago by ev970

Why do you need another method? The effect sizes that you get after running lfcShrink are moderated and shrunken, therefore suitable for ranking by effect size.

ADD REPLYlink written 10 days ago by ATpoint46k
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