Many thanks in advance for any help with this because i'm stratching my head. I am using Prostar for differential expression of shotgun proteomics data. As part of the process, I reduce the data down to FDR <1%, p-value <0.5 equivalent to a set of genes that are differentially expressed between my two conditions with no NA values at this point.
My issue is that when i move to the next step which is GO analysis, i get the error "Warning: Error in <-: NAs are not allowed in subscripted assignments" which i'm not sure what it means cause there should be no NAs in the differentially expressed dataset. GO analysis uses the package ClusterProfiler which is present in my packages so i dont thingk that is what is wrong.
I've updated the packages, R, R-studio, i'm tried to use different datasets, but i am still getting this message. This is extremely new to me and i would appreciate any advice or perhaps a fresh perspective.