I have two gene list as below, one of them is able to obtain an enriched KEGG pathway, the other one cannot.
I consolidate them to one list, and carry on the KEGG enrichment, none of pathway has been found.
The link of .Rdata of these lists, please use list, list_edge, list_limma to access.
https://bri.box.com/s/apc0nwdd57xymhatnngwg01w415rl2me
list_limma = list(doublePos_vs_singlePos_limma = DEG_doublePos_vs_singlePos_limma$ENTREZID,
doublePos_vs_singlePos_limma_Up = DEG_doublePos_vs_singlePos_limma_Up$ENTREZID,
doublePos_vs_singlePos_limma_Down = DEG_doublePos_vs_singlePos_limma_Down$ENTREZID,
doublePos_vs_doubleNeg_limma = DEG_doublePos_vs_doubleNeg_limma$ENTREZID,
doublePos_vs_doubleNeg_limma_Up = DEG_doublePos_vs_doubleNeg_limma_Up$ENTREZID,
doublePos_vs_doubleNeg_limma_Down = DEG_doublePos_vs_doubleNeg_limma_Down$ENTREZID)
list_edge = list(doublePos_vs_singlePos_edge = DEG_doublePos_vs_singlePos_edge$table$ENTREZID,
doublePos_vs_singlePos_edge_Up = DEG_doublePos_vs_singlePos_edge_Up$table$ENTREZID,
doublePos_vs_singlePos_edge_Down = DEG_doublePos_vs_singlePos_edge_Down$table$ENTREZID,
doublePos_vs_doubleNeg_edge = DEG_doublePos_vs_doubleNeg_edge$table$ENTREZID,
doublePos_vs_doubleNeg_edge_Up = DEG_doublePos_vs_doubleNeg_edge_Up$table$ENTREZID,
doublePos_vs_doubleNeg_edge_Down = DEG_doublePos_vs_doubleNeg_edge_Down$table$ENTREZID)
levels(list_limma) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
"doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")
levels(list_edge) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
"doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")
list = list(doublePos_vs_singlePos = c(DEG_doublePos_vs_singlePos_limma$ENTREZID,DEG_doublePos_vs_singlePos_edge$table$ENTREZID),
doublePos_vs_singlePos_Up = c(DEG_doublePos_vs_singlePos_limma_Up$ENTREZID,DEG_doublePos_vs_singlePos_edge_Up$table$ENTREZID),
doublePos_vs_singlePos_Down = c(DEG_doublePos_vs_singlePos_limma_Down$ENTREZID,DEG_doublePos_vs_singlePos_edge_Down$table$ENTREZID),
doublePos_vs_doubleNeg = c(DEG_doublePos_vs_doubleNeg_limma$ENTREZID,DEG_doublePos_vs_doubleNeg_edge$table$ENTREZID),
doublePos_vs_doubleNeg_Up = c(DEG_doublePos_vs_doubleNeg_limma_Up$ENTREZID,DEG_doublePos_vs_doubleNeg_edge_Up$table$ENTREZID),
doublePos_vs_doubleNeg_Down = c(DEG_doublePos_vs_doubleNeg_limma_Down$ENTREZID,DEG_doublePos_vs_doubleNeg_edge_Down$table$ENTREZID))
levels(list) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
"doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")
CompKEGG_limma <- compareCluster(geneCluster = list_limma, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)
CompKEGG_edge <- compareCluster(geneCluster = list_edge, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)
CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)
I can understand the principle of gene enrichment. I just so surprised about nonpathway can be matched because the list is approx 1000+, even without significance (I set pvalueCutoff = 1), should have some gene match to KEGG pathway. I doubt if the list feature causes the problem? I check several times, not conclude, so have to raise the question.
What's the error do you get when you reproduce my code?
In the compareCluster documents, I can't find the default qvalueCutoff setting. In the above situation, no enrichment can be found when pvalueCutoff = 1, but 2 enrichment show up when set q = 1. I suppose the default q had been set less than 1. Is that right?
yes, and the parameter list of
compareClusterdepends on thefunparameter. In your case, allenrichKEGGparameters can be passed tocompareCluster.