[BioC] limma read.maimages for scanarray express .csv files

[sltucker at artsci.wustl.edu]

Hi,

I am new to limma and am having problems reading Scanarray Express .csv
files into limma via read.maimages.  I am running R version 2.4.1 and
limma version 2.9.17.

I tried...

>RG<-read.maimages(files, source="scanarrayexpress", path=path)
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
	Specified column headings not found in file
In addition: Warning messages:
1: input string 1 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)
2: input string 1 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)
3: input string 1 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)
4: input string 1 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)

Adding in the column names doesn't seem to help, as I get the same error
when I try this (I have tried using "R"/"G" instead of "Rf"/"Gf" as well).

>RG<-read.maimages(files, source="scanarrayexpress", path=path,
columns=list(Rf="Ch1 Median", Rb="Ch1 B Median", Gf="Ch2 Median", Gb="Ch2
B Median"))

I have also tried including sep="," and using source="generic".  Removing
all the of header lines before the actual column names in the scanarray
output file doesn't fix the problem either.  What am I doing wrong?

Thanks,
Sarah