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z0on / GO_MWU

Rank-based Gene Ontology analysis of gene expression data
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Error in file(file, "rt") : cannot open the connection #10

Closed UsernameUrie closed 2 years ago

UsernameUrie commented 2 years ago

Hello,

I used these scripts on my own data several times, but since I got a new computer, I don't seem to be able to run it successfully. I tried with the data from heat.csv, without ANY modification once I saw it did not work with mine but the issu stays the same : error in file(file, “rt”) : cannot open the connection I assume the following message : cannot open file 'dissim0_MF_amil_defog_iso2go.tab': No such file or directory is just a consequence from the connection issu. I checked my Perl path, but I don't think it's the issue as Perl is installed in my C: drive and all the data is in my working directory (I checked). I tried to re-install all files to restart with clean files but it did not help.

Could you help me with this issue ? Thanks

Here's the code but as it is yours I'm not sure it's useful:

# Edit these to match your data file names: 
input="heats.csv" # two columns of comma-separated values: gene id, continuous measure of significance. To perform standard GO enrichment analysis based on Fisher's exact test, use binary measure (0 or 1, i.e., either sgnificant or not).
goAnnotations="amil_defog_iso2go.tab" # two-column, tab-delimited, one line per gene, multiple GO terms separated by semicolon. If you have multiple lines per gene, use nrify_GOtable.pl prior to running this script.
goDatabase="go.obo" # download from http://www.geneontology.org/GO.downloads.ontology.shtml
goDivision="MF" # either MF, or BP, or CC
source("gomwu.functions.R")

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 (gene-sharing) terms. See README for details.
#Alternative="g" # by default the MWU test is two-tailed; specify "g" or "l" of you want to test for "greater" or "less" instead. 
#Module=TRUE,Alternative="g" # un-remark this if you are analyzing a SIGNED WGCNA module (values: 0 for not in module genes, kME for in-module genes). In the call to gomwuPlot below, specify absValue=0.001 (count number of "good genes" that fall into the module)
#Module=TRUE # un-remark this if you are analyzing an UNSIGNED WGCNA module 
)
z0on commented 2 years ago

Hello - sorry about the delayed response, I am traveling - looks like the package is missing some of its files. Everything, including package files and your input files, should be in the same directory, and that directory must be the working directory in R. I feel this is what is causing problems? Misha

On Mar 14, 2022, at 10:48 AM, UsernameUrie @.***> wrote:

Hello,

I used these scripts on my own data several times, but since I got a new computer, I don't seem to be able to run it successfully. I tried with the data from heat.csv, without ANY modification once I saw it did not work with mine but the issu stays the same : error in file(file, “rt”) : cannot open the connection I assume the following message : cannot open file 'dissim0_MF_amil_defog_iso2go.tab': No such file or directory is just a consequence from the connection issu. I checked my Perl path, but I don't think it's the issue as Perl is installed in my C: drive and all the data is in my working directory (I checked). I tried to re-install all files to restart with clean files but it did not help.

Could you help me with this issue ?

Here's the code but as it is yours I'm not sure it's useful:

Edit these to match your data file names:

input="heats.csv" # two columns of comma-separated values: gene id, continuous measure of significance. To perform standard GO enrichment analysis based on Fisher's exact test, use binary measure (0 or 1, i.e., either sgnificant or not). goAnnotations="amil_defog_iso2go.tab" # two-column, tab-delimited, one line per gene, multiple GO terms separated by semicolon. If you have multiple lines per gene, use nrify_GOtable.pl prior to running this script. goDatabase="go.obo" # download from http://www.geneontology.org/GO.downloads.ontology.shtml goDivision="MF" # either MF, or BP, or CC source("gomwu.functions.R")

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 (gene-sharing) terms. See README for details.

Alternative="g" # by default the MWU test is two-tailed; specify "g" or "l" of you want to test for "greater" or "less" instead.

Module=TRUE,Alternative="g" # un-remark this if you are analyzing a SIGNED WGCNA module (values: 0 for not in module genes, kME for in-module genes). In the call to gomwuPlot below, specify absValue=0.001 (count number of "good genes" that fall into the module)

Module=TRUE # un-remark this if you are analyzing an UNSIGNED WGCNA module

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z0on commented 1 year ago

Just give the path to Perl executable as argument to gomwu_stats

On Wed, Jul 19, 2023 at 12:45 PM Marwa @.***> wrote:

@z0on https://github.com/z0on should I put perl in the system's PATH? not the working directory path?

— Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/10#issuecomment-1642500512, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZUHGGRNFCOSNZDXX5D3A3XRAMMXANCNFSM5QU7EHLQ . You are receiving this because you were mentioned.Message ID: @.***>

-- cheers Misha matzlab.weebly.com

marwa38 commented 1 year ago

working fine thanks Misha 💯