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

[Martin Morgan]

"Maya Bercovich" <MayaB at tauex.tau.ac.il> writes:

> Dear Sirs,

Please post to the Bioconductor list (see http://bioconductor.org for
instructions)

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

Please provide a short section of code that shows how you invoke the
function. It is very hard to tell what the cause of your problem is
without this.

read.maimages has a 'columns' argument. Do you supply it? If so, does
it contain the correct column names for the file type you are reading?
For instance, is the capitalization correct? The help page for
read.maimages provides some guidance.

> 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

Specific Bioconductor package versions work with specific R
versions. Instead of using install.packages, use

> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")

to get the right version for your R. For R 2.5.0, limma 2.10.5 is the
correct version. The limma author is very responsive to bug reports, so
seek additional help and if necessary report bugs rather than revert
to previous versions.

> Could this be the reason?

Please always provide the output of the command

> sessionInfo()

to provide a concise summary of your system.

> Thanks in advance
> Maya
>
>
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>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org