Hi all,

I would like to find which pathways are different between 2 groups. After getting very helpful support on this forum, I got advice to use egsea which combine some methods. However, I got this error:

    gsa = egsea(fit2, contrasts = contrast_matrix, gs.annots = gs.annots, baseGSEAs = baseMethods, sort.by = "avg.rank", num.threads = 4, report = FALSE)
EGSEA analysis has started
##------ Mon May  6 15:28:58 2024 ------##
Error in egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod,  : 
  (is(voom.results, "list") && "ids" %in% names(voom.results)) ||  .... is not TRUE
If I try to get voom.results from fit2:
geneIDs <- rownames(fit2$coefficients) 
testStats <- fit2$coefficients          
pValues <- fit2$p.value                
voom.results <- list(
  ids = geneIDs,
  t = testStats,
  p = pValues
gsa = egsea(voom.results, contrasts = contrast_matrix, gs.annots = gs.annots,
+             symbolsMap = v$genes, baseGSEAs = baseMethods, sort.by = "avg.rank", num.threads = 4, report = FALSE)
EGSEA analysis has started
##------ Tue May  7 15:17:18 2024 ------##
Log fold changes are estimated using limma package ... 
Error in runStandardLimmaDEA(voom.results, contrast, logFC.cutoff, fdr.cutoff) : 
  is(voom.results, "EList") is not TRUE
Googling this error but didn't find any helpful information. Seem fit2 is not an appropriate parameter in this case. Seem I need Large EList object to run but don't know how to get it. Monther Alhamdoosh haven't online on this forum for 5 years, so hope anyone ran this tool successful can help.
 Thank you so much!
                        
Thanks James! I update the question. The last question mean when we use buildIdx(), could we use gene symbol instead of entrezID. However, I decide to use entrezID as the vignettes for simplicity.
https://www.bioconductor.org/packages/release/bioc/vignettes/EGSEA/inst/doc/EGSEA.pdf
Yes, it is microarray data and I try egsea() first, egsea.ma() use different input.
                        
I tried egsea.ma and got this error:
gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.annots, baseGSEAs = baseMethods, sort.by = "avg.rank", num.threads = 4, report = FALSE)
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
It is hard to know which parameter is not correct in this case.