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

[Kasper Daniel Hansen]

On Jul 8, 2007, at 6:54 AM, Maya Bercovich wrote:

> Dear Sirs,
>
> How can I revert to an older limma version?
>
> Typing "install.packages("limma")"  in R gives a list of mirrors. How
> can I install the version I want after I obtain and untar the file  
> (e.g,
> limma_2.9.1.tar.gz)?

Not every version is kept around. You could try to see if 2.9.1 is  
part of a stable Bioc release. But in general I am not aware of how  
you can get any arbitrary old version of a package. When you have the  
tarball use
# R CMD INSTALL limma....
from the command line (and if that is not enough, look in this email  
list, the manual and the faqs for the numerous help available on this  
subject).

> I am running R 2.5.0 on a Linux machine (CentOS 5).  When using  
> limma it
> will not go past the read.maimages command.
>
> I get this error:
>
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>          Specified column headings not found in file

If you read this message carefully it seems that limma is looking for  
some columns in the file which does not exists.

>  In addition: Warning message:
> input string 1 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)

Coupled with this warning I guess that the first characters in your  
file are non-standard for example using a different alphabet or  
whatever.

You should look carefully at the file in order to see what the error is.

It could also be the local you are using: is he using english and you  
are using a different language?

> I was told by a colleague that this may be due to my limma version.
>
> I try to use limma 2.10.5 and he uses 2.9.1
>
> Could this be the reason?

Perhaps, but I doubt it.

>
> Thanks in advance
>
> Maya
>
>
>
>
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>
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