z0on
commented
3 months ago Hi - better late than never! I just noticed your issue open on github... Are you still having problems with this? It looks to me something is wrong with formatting of your GO annotations file: the script interprets it like all your genes are annotated with the same GO term. Misha
On Fri, Apr 19, 2024 at 9:15 AM MohHallal @.***> wrote:
Hello,
I'm new to transcriptomic analysis and I'm attempting to utilize GO_MWU on my dataset. I've followed the steps outlined in the guide, but I encountered an issue when executing the "Calculating stats" section of the GO_MWU.R file. The error message I received is as follows: `gomwu_b: cannot create output dissim0MF/the_path_to/amil_defog_iso2go.tab the_path_to/amil_defog_iso2go.tab the_path_to/heats.csv MF largest=0.1 smallest=5 cutHeight=0.25
Run parameters:
largest GO category as fraction of all genes (largest) : 0.1 smallest GO category as # of genes (smallest) : 5 clustering threshold (clusterCutHeight) : 0.25
retrieving GO hierarchy, reformatting data...
go_reformat: Genes with GO annotations, but not listed in the measure table: 55960 Terms without defined level (old ontology?..): 0
go_nrify: 1 categories, 6777 genes; size range 5-677.7 0 too broad 0 too small 1 remaining
removing redundancy:
calculating GO term similarities based on shared genes... Error in file(file, "rt"): cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'dissim0MF/the_path_to/amil_defog_iso2go.tab': No such file or directory ` Is this a common error, and how can I fix it? Note that I am using ubuntu and "the_path_to" refers to the directory containing all the necessary inputs and the files of GO_MWU.
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Hello,
I'm new to transcriptomic analysis and I'm attempting to utilize GO_MWU on my dataset. I've followed the steps outlined in the guide, but I encountered an issue when executing the "Calculating stats" section of the GO_MWU.R file. The error message I received is as follows:
`gomwu_b: cannot create output dissim0MF/the_path_to/amil_defog_iso2go.tab the_path_to/amil_defog_iso2go.tab the_path_to/heats.csv MF largest=0.1 smallest=5 cutHeight=0.25
Run parameters:
largest GO category as fraction of all genes (largest) : 0.1 smallest GO category as # of genes (smallest) : 5 clustering threshold (clusterCutHeight) : 0.25
retrieving GO hierarchy, reformatting data...
go_reformat: Genes with GO annotations, but not listed in the measure table: 55960
Terms without defined level (old ontology?..): 0
go_nrify: 1 categories, 6777 genes; size range 5-677.7 0 too broad 0 too small 1 remaining
removing redundancy:
calculating GO term similarities based on shared genes... Error in file(file, "rt"): cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'dissim0MF/the_path_to/amil_defog_iso2go.tab': No such file or directory `
Is this a common error, and how can I fix it? Note that I am using ubuntu and "the_path_to" refers to the directory containing all the necessary inputs and the files of GO_MWU.