Alexey Sergushichev
Alexey Sergushichev
When the input statistic is unbalanced (skewed towards positive or negative values) it's hard to accurately estimate two-tailed GSEA p-value. By Subramanian et al it is normalized by the probability...
> Thank you, I created the ranks based on a list of differentially expressed genes using this metric: -10logFDR * (+/- from FC). Based on this ranking I have 8015...
> I have a related question about this error (I hope it's ok that I place it here). I am getting this error while using logFC, but in my case...
Hi, Can you, please, attach the data so that I can reproduce the error?
Thanks, I can reproduce the problem. Quickfix is to remove NA-ranked genes: ``` ranked_genes
Not sure, haven't dug deeper yet. I guess it's just mishandling of NAs somewhere in the code.
@nsbc6 you should put all the expressed genes into fgsea, not just a small subset which you apparently have.
I wouldn't say 34 is reasonable amount of genes for GSEA. But formally, one of your input pathways contain all of these 34 genes, which crashes GSEA, as we can't...
Hi, `exampleRanks` is moderated t-statistic, not log2FC, but has the same direction. > ES means "A positive ES indicates gene set enrichment at the top of the ranked list; a...
Hi, Can you give an example, which is not working now because of use of `theme_bw`? I've tried, and it looks like you can change things after, like doing: ```...