This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in mitch in R

Error in mitch in R

I am trying to perform mitch analysis, I have the results tables (I convert them to text files), I downloaded the gmt file (symbols) and the results table has gene symbols also. I got an error, what should be done to fix it? Thanks

This is the res1 text file enter image description here

x <- list("res1"= res1, "res2"= res2)

y <- mitch_import(x, DEtype="DESeq2")

res <- mitch_calc(y,hallmarks_symbols , priority="significance")

Warning: No results found. Check that the gene names in the
            profile match the gene sets and consider loosening the minsetsize
            parameter.
mitch symbols gene r
• 1,239 views • link
updated by rpolicastro rpolicastro • written by Amr • Amr

Instead of sharing a screenshot copy and paste the data into a code block.

• 0 views • link
written by rpolicastro rpolicastro

I did it, its res1 in that code: x <- list("res1"= res1, "res2"= res2)

Maybe there is something wrong in the res1 file that's why I shared the screenshot

• 0 views • link
written by Amr • Amr

1 answer

The solution is to add geneIDcol in :

y <- mitch_import(x, DEtype="DESeq2", geneIDcol = "GeneSymbol")
• 0 views • link
updated by rpolicastro rpolicastro • written by Amr • Amr

Log in to answer this question.

More posts like this