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Metabolomics Society Forum

Software => R => XCMS => Topic started by: Jeffomics on September 16, 2013, 11:43:05 AM

Title: Error from running "reporttab"
Post by: Jeffomics on September 16, 2013, 11:43:05 AM
After filling the missing peaks, I ran the following command to analyze my dataset.

Code: [Select]
> reporttab <- diffreport(xset3, "Prestudy", "Poststudy", "HopkTrial_1", 10, metlin=0.15, h=480, w=640)

Unfortunately, XCMS comes back with the following message:

Quote
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'HopkTrial_1.tsv': Permission denied

Is there any one who can help me define the reasons for the error message?  Your prompt response will be highly appreciated.

Best wishes,

Jeff
Title: Re: Error from running "reporttab"
Post by: hpbenton on September 16, 2013, 12:59:20 PM
Jeff,

The directory you're in you don't have permission to write a file. In unix/Linux just write to you're home directory so you can use

Code: [Select]
reporttab <- diffreport(xset3, "Prestudy", "Poststudy", file="~/HopkTrial_1", 10, metlin=0.15, h=480, w=640)

In windows the easiest way is to change directory to your use the file tab and then rerun the command. Should work but let us know.

Paul
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