[BioC] LIMMA

[Gordon Smyth]

>[BioC] LIMMA
>Matt Settles mattsettles at moscow.com
>Mon Jan 30 19:10:12 CET 2006
>
>Hello all,
>
>I've found an issue in your limma package concerning read.maimages
>
>First there appears to be two different latest versions out there CRAN has
>limma 2.4.7 and bioconductor has 2.2.0 is 2.4.7 still experimental or has
>bioconductor just not been updated.

Please read Section 2.2 "Installation" of the Limma User's Guide.

The second paragraph of http://www.bioconductor.org/whatisit will 
tell you a little about the Bioconductor release cycle.

>Issue with read.maimages, wt.fun no longer works.

It works fine for me in limma 2.4.7. Others with whom I've checked 
are also having no problems.

>Since read.table is now using colClasses you include wt.fun in its creation
>which is a function and not a column and therefore error outs.
>
>Possible fixes could include removing colClasses entirely and read.table
>reads in all columns, or
>
>Remove wt.fun from colClasses creation and require user to include all
>columns found in wt.fun in other.columns, or
>
>Its your program do whatever you want
>
>Just thought you'd like to know

Thank you for taking the trouble to write in. But reports are only 
useful if you give example code sufficient to reproduce the problem. 
In most cases apparent bugs are actually user errors, and giving the 
code will allow us to tell you how to avoid the problem.

You also need to specify your operating system and R version. 
sessionInfo() is any easy way to show versions of R and attached 
packages. See the posting guide at 
http://www.bioconductor.org/docs/postingGuide.html.

Best wishes
Gordon

>Matt Settles
>University of Idaho
>Department of Bioinformatics and Computational Biology