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Groups. webgestalt. Contact owners and managers. 1–30 of 257. . Welcome to Webgestalt user forum! 0 selected. seb...@gmail.comJohn Elizarraras2. Aug 8.
Mar 12, 2024 · to webgestalt Hi there, I'm trying to running an analysis of my DEGs but when i enter it i notice that genes in the downregulated bar are, instead, upregulated.
Jul 28, 2022 · There is an option for it in the expandable "advanced parameters" section in the submission form. But if you didn't change it, it should be "BH" or Benjamini-Hochber.
Sep 16, 2020 · Yuxing Liao. Mar 9, 2021, 2:37:55 PM. to Mario Ezquerra, webgestalt. I think you can look into the GSEA plot to see the rank distribution. It is likely the genes above the cutoff used for ORA are not concentrated near the top of the rank list. Basically ORA will consider them equally but GSEA takes score and rank into consideration.
May 10, 2023 · to webgestalt. Unless you directly permute the gene ranks instead. Apologies if I overlooked it ...
Oct 5, 2023 · to webgestalt. I am using the web gestalt API for R. One of the sets of data I run through ORA for BPs ...
Jun 20, 2019 · A few lines in your input file have an empty gene ID, for example line 1202. Currently, it is stringent and checks every line to have 2 columns. I probably can change it to a percentage cutoff. Yuxing. You received this message because you are subscribed to the Google Groups "webgestalt" group.
Mar 13, 2023 · For webgestalt, the rnk file needs have IDs in the first column and the score in the second separated by a tab. In excel, you can do this by saving as a "Tab delimited Text (.txt)" file. Then you have to rename the file ending into .rnk. It sounds like you may have done this already. If you have, you can try double checking that there are no ...
Feb 26, 2019 · 3. Finally, I did an experiment and ran the human example run, which works but when I copy and paste the data set into a text file and try to upload it as an RNK file, it does not work, which would suggest some aspect of the uploading file process does not work.
Dec 6, 2023 · In most cases, it is simple. 20 will show 10 positive and 10 negative sorted by FDR. It could be 10 positive and 5 negative if there are just 5 significant gene sets in the negative direction.
