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z0on / GO_MWU

Rank-based Gene Ontology analysis of gene expression data
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gomwu_b: cannot create output dissim0_BP_ #4

Closed shellywanamaker closed 4 years ago

shellywanamaker commented 4 years ago

Hello,

I continue to get the following error thrown by the gomwu_b.pl script and I'm not sure what's going on. Any advice is appreciated, thanks! -Shelly

gomwuStats(input, goDatabase, goAnnotations, goDivision,

z0on commented 4 years ago

Hi Shelly - too easy! try putting your input file into the directory where all the script files are and run it using the input file name without path (i.e, just “silo23_all_pro_GO.tab”) Mish

On Sep 14, 2019, at 10:19 PM, Shelly Trigg notifications@github.com wrote:

Hello,

I continue to get the following error thrown by the gomwu_b.pl script and I'm not sure what's going on. Any advice is appreciated, thanks! -Shelly

gomwuStats(input, goDatabase, goAnnotations, goDivision,

perlPath="perl", # replace with full path to perl executable if it is not in your system's PATH already largest=0.1, # a GO category will not be considered if it contains more than this fraction of the total number of genes smallest=5, # a GO category should contain at least this many genes to be considered clusterCutHeight=0.25) # threshold for merging similar gomwu_b: cannot create output dissim0BP/Users/Shelly/Documents/GitHub/OysterSeedProject/analysis/UniprotAnnotations_NetworkAnalysis/ASCA_logNSAFs_FunctionalAnalysis/silo23_all_pro_GO.tab — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/4?email_source=notifications&email_token=ABZUHGGPOA4ZDAAKMNZQBGDQJWSVRA5CNFSM4IWY72I2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HLNDSSQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGCU5YXW3ZB3ZM6MKDDQJWSVRANCNFSM4IWY72IQ.

shellywanamaker commented 4 years ago

Hey Mish, all my input files are in the directory where all the script files are. I'll try removing the path and see if it runs. I also found some formatting discrepancies in my input file (it included column names and there were "; " separating each GO term. Hopefully it works after these changes. Thanks for your quick response!

z0on commented 4 years ago

that error definitely was because the input filename included path, but hey, there always could be other errors as well! :) please don’t hesitate to ask

On Sep 14, 2019, at 10:46 PM, Shelly Trigg notifications@github.com wrote:

Hey Mish, all my input files are in the directory where all the script files are. I'll try removing the path and see if it runs. I also found some formatting discrepancies in my input file (it included column names and there were "; " separating each GO term. Hopefully it works after these changes. Thanks for your quick response!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/4?email_source=notifications&email_token=ABZUHGDMCFS4HK73U3TJDMDQJWVZ5A5CNFSM4IWY72I2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6XIRDI#issuecomment-531531917, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGEUFCKZLI4PVPZN67LQJWVZ5ANCNFSM4IWY72IQ.

shellywanamaker commented 4 years ago

it worked! thanks so much!