[BioC] A question about the Marray Package

Robert Gentleman rgentlem at fhcrc.org
Wed Jul 13 17:00:19 CEST 2005


Tony Kowal wrote:
> Hi All, 
> I am trying to read in microarray data from a two-color platform using the Marray package.  One of
> the commands that I have used to read in data (with R 2.0 and R2.01) is not working for me with
> R2.1.  I was wondering if anyone has encountered this problem, and can tell me how to fix the
> problem.  Thanks very much in advance for your help.
> I use the "fnames" command to specify that I wish to read in a SPOT file: 
>>fnames <- dir(path = datadir, pattern = paste("*", "spot", sep = "."))
> and I receive the following error message: 
> Error in list.files(path, pattern, all.files, full.names, recursive) : 
>         invalid 'pattern' regular expression

  Which means just what it says. What you used is not a valid regular 
expression and while it did work for a while it was not valid. R fixed 
its regular expression handling - and some things like this have stopped 
working (but they should never have worked in the first place).

  paste(".*", "spot", sep=".")
  is probably what you intended in the first place, but you might want 
to look at a reference on regular expressions to be sure.

> As I mentioned, the fnames command as I typed above has worked in earlier versions of R, but seems
> to be a problem with R2.1.

the output of sessionInfo would be of much more help here.


> I am using a PC running Windows XP, R2.1.
> Thanks -
> Tony
> Tony Kowal
> Graduate Student
> Rex Chisholm Laboratory
> Northwestern University
> 303 E. Superior 
> Lurie Building
> Room 7-250
> Chicago, IL 60611
> Lab: 312 503 4169
> e-mail: askowal at northwestern.edu
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