Guido Hooiveld

Results 234 comments of Guido Hooiveld

change edge color in cnetplot

Got some time to prepare some examples. See also these threads: https://github.com/YuLab-SMU/enrichplot/issues/302#issuecomment-2517971618 and https://github.com/YuLab-SMU/enrichplot/issues/293#issuecomment-2462502566 ``` > ## load libraries > library(clusterProfiler) > library(enrichplot) > library(org.Hs.eg.db) > > ## load example...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

Next time please properly format your post! Yet, I cannot reproduce your problem! ``` > library(clusterProfiler) > library(org.Hs.eg.db) > > data(geneList, package="DOSE") > > res > res # # Gene...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

Again, it is working for me....! Does the exact same code from me also work for you? (copy/paste it) Note; for your specific dataset: - which warnings are returned? -...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

Once more, that is working for me as well! - Please report back; what did you change so that it works now when analyzing a single dataset? - Which version...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

Some thoughts: Since you got he error when analyzing the included human dataset, and I do not, it points to an issue with your `R/Bioconductor` installation. Also, are you running...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

I am lost... I have the same version of `clusterProfiler` as you have installed, and it works fine for me... ``` > packageVersion("clusterProfiler") [1] ‘4.12.0’ > ``` Yet, I am...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

So: - you have the latest version of `R`, `Bioconductor` and `clusterProfiler` installed. [Just to be sure; run once more as administrator in a freshly started session of `R` this...

"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

One last remark: Again, be sure to also run the code in `R` 'only' (and not through `R-studio`)! Another user just reported that this solved his/her problem, although that problem...

ERROR in enrichGO,when seting ont = "ALL",Error in data.frame(..., check.names = FALSE) : 行名里有缺失值。

It is working in my hands with the example code. See below. I noticed you are indeed using the latest version of `clusterProfiler` (i.e. `4.12.2`), but maybe your Bioconductor installation...

ERROR in enrichGO,when seting ont = "ALL",Error in data.frame(..., check.names = FALSE) : 行名里有缺失值。

Could you please post your code, error and `sessionInfo()`. Also, does the example code work for you?