[BioC] readGenericHeader problem in limma 2.7.8?

[Gordon K Smyth]

Dear Bobby,

I've tried the code you give below on a GenePix gpr file, and it works fine in limma 2.7.9.  So
the problem does not appear to be a change in limma.

I assume that when you run the code that "B635 Median" is on one line rather than wrapped across
two lines as in the email.  Wrapping it over two lines would cause the error your report.

Best wishes
Gordon

> Date: Mon, 21 Aug 2006 15:12:34 -0400
> From: Bobby Prill <rprill at jhu.edu>
> Subject: [BioC] readGenericHeader problem in limma 2.7.8?
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <0C3B6476-5D01-4F19-A795-0B9787C3DA8A at jhu.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> 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.