gseGO for multiple groups

Question

[Omics data mining]

I would like to perform the gseGO on DEGs belonging to multiple groups. I am using gseGO within clusterprofiler package . I prepared the input as per the requirement and sorted geneList based on foldchange.

mydf <- data1

mydf1 <- data.frame(Entrez=names(mydf), FC=mydf)

mydf1 <- mydf1[abs(mydf1$FC) > 1,]

mydf1$group <- "upregulated"

mydf1$group[mydf1$FC < 0] <- "downregulated"

mydf1$othergroup <- "1"

mydf_2 <- data2

mydf_2 <- data.frame(Entrez=names(mydf_2), FC=mydf_2)

mydf_2 <- mydf_2[abs(mydf_2$FC) > 1,]

mydf_2$group <- "upregulated"

mydf_2$group[mydf_2$FC < 0] <- "downregulated"

mydf_2$othergroup <- "2"

rlist <- rbind(mydf1,mydf_2)

rlist <- rlist[order(rlist$FC, decreasing = TRUE),]

formula_res <- compareCluster(Entrez~group+othergroup, data=rlist, fun="gseGO", OrgDb = "org.Hs.eg.db")

**But I am getting following error :

formula_res <- compareCluster(Entrez~group+othergroup, data=rlist, fun="gseGO", OrgDb = "org.Hs.eg.db") Error in GSEA_internal(geneList = geneList, exponent = exponent, minGSSize = minGSSize, : geneList should be a decreasing sorted vector...**

I would appreciate all the suggestions.

[Basti]

You might need to update your clusterProfiler package and have a look at your formula which is not the one requested in the vignette : https://rdrr.io/github/GuangchuangYu/clusterProfiler/man/compareCluster.html

[Omics data mining]

Thanks alot. I updated my clusterProfiler and got significant gseGO terms by using

res <- compareCluster(geneClusters=inputList, fun = "gseGO") .

Next, I tried to develop enrichplot from the output by using :

test.out <- enrichplot::pairwise_termsim(res)

emapplot(test.out)

BUt it gives "Error in $<-.data.frame(*tmp*, "Cluster", value = NA_integer_) : replacement has 1 row, data has 0"

But my output consist of various enriched terms as you see in the text below :

$ ID : chr "GO:0002377" "GO:0050853" "GO:0050871" "GO:0016064" ... $ Description : chr "immunoglobulin production" "B cell receptor signaling pathway" "positive regulation of B cell activation" "immunoglobulin mediated immune response" ...

$ setSize : int 68 51 53 68 69 84 72 193 119 28 ...

$ enrichmentScore: num 0.754 0.772 0.718 0.668 0.663 ...

$ NES : num 2.87 2.75 2.58 2.54 2.53 ...

$ pvalue : num 1e-10 1e-10 1e-10 1e-10 1e-10 ...

$ p.adjust : num 5.84e-08 5.84e-08 5.84e-08 5.84e-08 5.84e-08 ...

$ qvalues : num 5.35e-08 5.35e-08 5.35e-08 5.35e-08 5.35e-08 ...

$ rank : num 827 581 749 842 842 581 526 777 599 581 ...

$ leading_edge : chr "tags=65%, list=14%, signal=57%" "tags=59%, list=10%, ....

I tried various option but every time I am getting same error and not able to fix it.
I would appreciate your suggestion.