[BioC] how to revert to an older limma version?

[Martin Morgan]

Hi Maya --

I am glad that Sys.setlocale("LC_ALL", "en_US") allowed you to read
most files.

>> RG1 <-read.maimages(targets.RG1$Filename,columns=list(Rf="F635Median",Gf="F532Median",Rb="B635Median",Gb="B532Median"), path=path)
>
> Read /mnt/lifestore/Biotech/DannyS_Shared/Users/Revital/ssdp//B12Z0471_A.gpr
>
> (…all the other .gpr files are read, until: )
>
> Read /mnt/lifestore/Biotech/DannyS_Shared/Users/Revital/ssdp//B12J0504_A.gpr
>
> Error in readGenericHeader(fullname, columns = columns) :
>
>         Specified column headings not found in file

I guess the obvious question is: are the column names present in the
.gpr file? The files are processed in the order given in
targts.RG1$Filename, so you can figure out which file is causing
problems, open it in a text editor and look for the column names that
you provide. Do NOT use your text editor's 'Save' function, as this
could make unexpected changes to the file.

Two e-mail tips:

1. Use 'reply all' or similar to reply to the list. This keeps the
email in 'threads' that make it possible to follow different issues
(see the archive at
https://stat.ethz.ch/pipermail/bioconductor/2007-July/thread.html for
examples of this)

2. With 'Reply all', most email clients will insert a '>' at the start
of each line. This is very helpful to follow different conversations,
for example:

>> First email
> Second email, responding to first email
Third email, responding to first


Best of luck,
-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org