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No gene can be mapped when using enrichKEGG #561
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I can confirm, I am experiencing the same issue with a script that I haven't touched for 9 months.
Session Information:
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Converting the entrez ID's does not seem to help either.
This is kinda stinky, I need this figure for my Dissertation which is supposed to go to comittee on Monday evening I may try and revert to a previous version. |
Upgrading BioConductor to the most current version fixed this for me. |
Had to reinstall R from scratch to the last version, and also Bioconductor and also all possible packages to the last versions and it worked |
Same problem. Do I have to upgrade or downgrade the package to a certain version? |
I updated all and hoped for the best (that other scripts I usevwill keep working)...also update/installed all packages required by the installation of clusterProfiler since I could not be sure of what is critical and what not |
搞死人的,新版本要最新的DOSE,只能升级整个R,还要重装调整之前所有包的兼容性,真的醉了。 |
所以它看起來 :) |
I updated Bioconductor, clusterProfiler and DOSE and still got error as mentioned before
DOSE v3.24.2 |
I got the same issue, even though the packages are updated to the latest version. R 4.2.2 |
FYI
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@dppss90008 Sweet, this works!! |
the problem is the function OrganismMapper. |
Sweet, this workaround did the trick. Do we need to update everything to make it work without the local DB? thanks |
I debuged the code step by step, and located the bug: |
you missed a step see above, that is why it is going to cache. |
Hello, I tried to re-install with
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HERE: You need to update the DOSE package\install version 3.23.2 O try some of the previously suggested solutions |
It's work for me! thank you |
Please, how to update the DOSE package to version 3.23.2 ? I don't want to update my R to version 4.2. |
I have the same problem with "no genes mapped" when using the gseKEGG from ClusterProfiler. Everuthing worked fine a month ago I have tried updating bioconducter to the newest version 3.16. How to check that? Can someone guide me to a solution (I am relative new in R so it needs to be for dummies :D ) |
Solved - I restarted R and then the updates were done and the Code works again |
Same problem, but if I use |
@DavideBrex Please make sure you are using the latest version of clusterProfiler and please provide your sessioninfo. |
I am facing the same issue also with latest version |
I am using last version. Thank you for the support.
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@DavideBrex From the sessioninfo, I see your DOSE is not the release version, please update it. If you still report an error, you can try using the createKEGGdb: #561 (comment) |
I copied and ran @dppss90008 above scripts. However, I got the below error. I believe there is something wrong with the createKEGGdb code. Can you please check it? Thanks!
Error in clusterProfiler:::kegg_list("pathway", i) : unused argument (i) |
@Wenjuan-ZHU createKEGGdb is OK. Please update your clusterProfiler. |
@huerqiang Thanks! it works after I reload clusterProfiler. |
Cool, man. It is useful, but I ended up switching the R version, then using the latest clusterProfiler, it wored out. |
Got error in the first step.
Switched to this way:
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Hi, Thanks all re: above as I thought I was losing the plot when I couldn't get gseKEGG to work! However, I still can't- and this is likely a version issue for me as I am currently in the final write-up phase of my PhD and can't risk updating R beyond the one I'm running (v4.2.1)- therefore I think my clusterProfiler and DOSE packages are as up to date as they can be (clusterProfiler_4.4.4, DOSE_3.22.1). Running the createKEGGdb::create_kegg_db(species) gives me the same error as Wenjuan-ZHU had. Is there another work around I can use? I have downloaded the KEGG gmt file from the MSig database. Is there a way to read that in using createKEGGdb? Thanks in advance. |
I am using clusterProfiler 4.9.3.2 but still have the same issue: |
@Cristinex Please show your code and seeioninfo. |
I am using the enrichKEGG function, but my code, that was working last week does not work anymore.
Also the example in the vignette doesn't work anymore:
data(geneList, package="DOSE") #Vignette example
gene_names <- names(geneList)[abs(geneList) > 2]
kegg_enrich <- enrichKEGG(gene = gene_names, organism = "hsa", pvalueCutoff= 0.05, qvalueCutoff= 0.2)
--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL...
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