[BioC] readGenericHeader problem in limma 2.7.8?

Bobby Prill rprill at jhu.edu
Mon Aug 21 21:12:34 CEST 2006


There seems to be a problem with read.maimages() in the current  
release version of bioconductor (1.8).  I need load a "generic" gpr- 
like file using the column headers.

The following code used to work, but now is broken:

library(limma)
cols = list(Rf="F635 Median",Gf="F532 Median",Rb="B635  
Median",Gb="B532 Median")
RG = read.maimages("mydata.gpr", columns=cols)

Is this a bug?  How can I get around this problem?

I have tried
limma version 2.7.8 and 2.7.9

I'm on a Mac OSX 10.4.7
Running R.app 1.16

The error message is:
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
         Specified column headings not found in file
In addition: Warning message:
input string 1 is invalid in this locale in: grep(pattern, x,  
ignore.case, extended, value, fixed, useBytes)

Even though it says it can't find the headers, I know they are  
there.  This error started to occur when I installed a fresh copy of  
Bioconductor 1.8 after my disk crashed.  I was probably running 1.7  
before that.

I don't know how to attempt an install of 1.7 to see if that affects  
anything.

Thanks for the help.



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