[BioC] Help strange GSEA error

Martin Morgan mtmorgan at fhcrc.org
Wed May 2 18:01:22 CEST 2012

On 04/30/2012 09:26 AM, Alejandro Quiroz wrote:
> Hi Chris
> I'm Alejandro Quiroz, from the Department of Biostatistics at Harvard University
> Did you ever solve the issue about:
>> source('basicGSEA.R')
> 'envir' chosen:<environment: R_GlobalEnv>
> encoding = "native.enc" chosen
> Error: '\%' is an unrecognized escape in character string starting "Tag
> \%"
> ?
> I'm having the same thing with R-GSEA from :http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/R-GSEA_Readme

Hi Alejandro --

Probably you should ask the people responsible for the script, but 
perhaps it helps to ensure that your 'locale' is C, e.g.,


on many systems. Also working through the 'encoding' argument to 
source() might be helpful, ensuring too that you have not inadvertently 
converted a simple text file to a file with an unexpected encoding. The 
output of sessionInfo() and a reproducible example are always helpful.


> I would greatly appreciate if you respond!
> Thanks
> Alejandro
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

More information about the Bioconductor mailing list