[BioC] Re: Limma GUI exporting

[James Wettenhall]

Hi Seby,

On Wed, 23 Jun 2004, Seby wrote:
> I am using LimmaGUI for a micro array data analysis..Is there anyway I can 
> export the M values for all genes along with the gene names...right now It 
> exports M values but doesnt have the gene names or ID columns..

I've just uploaded a new version of limmaGUI (1.1.4) to:
http://bioinf.wehi.edu.au/limmaGUI/
which has this feature you have requested.

You can install it with:
install.packages("limmaGUI",contriburl="http://bioinf.wehi.edu.au/limmaGUI")

after checking that 
.libPaths() 
gives an appropriate R library directory for installation.

limmaGUI now includes all columns from the GAL file when it 
exports M values or A values, and while the format is still the 
same (tab-delimited text), the default file extension is now 
".xls", so that you can double-click on the file and it will 
open up automatically in Excel. (The ".xls" extension for 
tab-delimited text is also used in other places, e.g. the 
Stanford Microarray Database.)

Also, "Export M" and "Export A" now appear in the "File" menu, 
just above "Export HTML Report".  They will eventually be 
removed from the "Normalization" menu.

I'll do something similar for affylmGUI soon.

Another thing on my "TO DO" list for limmaGUI is to make the GAL 
file optional like it is in limma.  It makes sense to require a 
GAL file for "Spot" image analysis files which is what I started 
out using, but it shouldn't be required for other formats like 
"ImaGene".

Regards,
James