download_KEGG {clusterProfiler} cannot get the right pathway map

[china-fix]

Dear Professor Yu, i recently meet the problem with 'enrichKEGG()' or 'createKEGGdb::create_kegg_db()' method, which cannot correctly get the pathway map, could it be a bug form the download_KEGG {clusterProfiler} , see the example below:

kk <- enrichKEGG(gene = gene, organism = "ece", keyType = "kegg", pAdjustMethod = 'fdr')

Reading KEGG annotation online: "https://rest.kegg.jp/link/ece/pathway"... Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway"... --> No gene can be mapped.... --> Expected input gene ID: --> return NULL...

why Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway"..., according to my understanding, it should be Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/ece"... in this case

Kind Regards Xiao

[jsnagai]

Also facing the same issue here

[jsnagai]

@china-fix install the current github version, the issue is addressed in the new commit

devtools::install_github("YuLab-SMU/clusterProfiler")

[china-fix]

@china-fix install the current github version, the issue is addressed in the new commit

devtools::install_github("YuLab-SMU/clusterProfiler")

@jsnagai Thanks bro, i saw a the new commit! cheers!

[ZZhenQi]

thanks a lot. But i also have a problem is that after kk analysis, dotplot did not works:

dotplot(kk,showCategory = 20) Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero

[ZZhenQi]

thanks a lot. But i also have a problem is that after kk analysis, dotplot did not works:

dotplot(kk,showCategory = 20) Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero

I found that the dotplot did not plot the result because the qvalue was greater than 0.05

[yangxinzhi]

But there seems to be a problem, the result is that there is no significant path

[ZZhenQi]

Dear Professor, Yes， I also found that the enrichKEGG@results：p.adjust and q values, the value both were 0.999, may be not correct. The description is very long including Species Information.

best regards

[guidohooiveld]

@ZZhenQi: it is not uncommon to observe identical values of p.adjust and qvalue for variables (genes, proteins, gene sets) despite having a different pvalue. See e.g. this thread at the Bioconductor support forum for more details on this: https://support.bioconductor.org/p/104789/

[ZZhenQi]

@ZZhenQi: it is not uncommon to observe identical values of p.adjust and qvalue for variables (genes, proteins, gene sets) despite having a different pvalue. See e.g. this thread at the Bioconductor support forum for more details on this: https://support.bioconductor.org/p/104789/

Thank you very much！