assaron
commented
3 years ago Hi, there should be a warning message, describing why you get NAs and probably even a way fix the problem. Likely, your gene-level statisitic has a skewed distribution.
On Tue, Jul 6, 2021, 20:27 Paul Stewart @.***> wrote:
Hello, I am running fgsea on some RNA-seq data with parameters minSize = 15, maxSize = 500, scoreType = "std", and eps = 1E-50. I am getting some NA's in the pval results column. These gene sets are a little on the large side, but they are under my maxSize. They seem to be the only ones with this issue. Below is the data sorted so that you can see the NA's. Could you help me understand what the issue might be? Thank you.
[image: Screen Shot 2021-07-06 at 1 26 29 PM] https://user-images.githubusercontent.com/5620536/124642392-cb5b1180-de5d-11eb-8dc3-d462221816dd.png
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pstew
Hello, I am running fgsea on some RNA-seq data with parameters minSize = 15, maxSize = 500, scoreType = "std", and eps = 1E-50. I am getting some NA's in the pval results column. These gene sets are a little on the large side, but they are under my maxSize. They seem to be the only ones with this issue. Below is the data sorted so that you can see the NA's. Could you help me understand what the issue might be? Thank you.