Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent

Question

[Chris]

Hi all,

I would like to find which pathways are different between 2 groups. I got advice to use egsea which combine some methods. However, I 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

Googling this error but didn't find any helpful information. Author of the tool haven't online on this forum for 5 years, so hope anyone ran this tool successful can help. Thank you so much!

[1769mkc]

https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list

[Chris]

Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The support page of the tool is not very active if a user have question. I think the way metascape work for pathway analysis is similar enrichGO() which we can't choose a gene set we would like to analyze such as c2 gene set from MSigDB.

[1769mkc]

"c2 gene set from MSigDB." this i agree in that case https://bioconductor.org/packages/release/bioc/html/fgsea.html you can try this one which what you need if i remember it using

[Chris]

Thanks 1769mkc! I also tried fgsea. The author of limma comment on this post that p value from fgsea is not truly significant as it is https://support.bioconductor.org/p/9158100/#9158140. Which he recommend to use camera(). The thing is that result from camera(), fgsea() or gsva() is different. Which the author of gsva() recommended egsea() which combine several pathway analysis tool include camera() and gsva().

[1769mkc]

please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help