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First of all, thank you immensely for this wonderful library. I'm a Python lover and hate the irregularities of R. It gladdens me to see this library constantly growing and implementing many bioinformatic functionalities once only available at R. Please keep up the good work! Now, I've got someone asking how exactly the FDR value being displayed in the normal signal-to-ratio GSEA plots is calculated. According to the GSEApy documentation, I guess p-values are corrected using Benjamini–Hochberg procedure where alpha is set at 0.05 if I used unmodified GSEApy modules (I am no expert of statistics, by the way). Am I correct? Thank you in advance! |
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Replies: 1 comment 1 reply
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Hi BroMynn, Sorry for replying late. For the FDR implementation for GSEA, it's not the same as Benjamini–Hochberg procedure. I have followed the same strategy in the R (see here), which is same as the original paper used. Hope this helps |
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I see, thank you very much! |
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Hi BroMynn,
Sorry for replying late. For the FDR implementation for GSEA, it's not the same as Benjamini–Hochberg procedure. I have followed the same strategy in the R (see here), which is same as the original paper used.
Hope this helps