[BioC] Different results Limma vs LimmaGUI?

[J.delasHeras at ed.ac.uk]

Hi,

I have been using LimmaGUI for a while, and I am starting to use Limma 
directly, and I was comparing the results I get with both methods, to 
make sure I am doing things right.

The lists of genes I am getting are roughly the same, but the orders do 
change a bit, and so do the B values (that I use to rank the genes).

Is this expected, perhaps because different limma versions do 
calculations in slightly different ways? or is that an indication that 
I am not doing the analysis in the same way?

For LimmaGUI, I use the latest (July 2005), version 1.3.9 (which uses 
limma 2.0.2) on R 2.1.1
Limma, I am using version 2.2.0 with R 2.2.0 (both latest)

In one experiment (two slides only) I get a B max of 6.33 with limma, 
and 6.92 with LimmaGUI. Another 3.13 with limma, and 2.84 with 
LimmaGUI. Then I add another 3 slides (5 total now) and the B max 
increases to 13.0 in both limma and limmaGUI. So, the differences are 
not big... is this due to slight changes in the way successive versions 
of limma do certain calculations?

The analysis included:
- bkg correction: substract
- within arrays normalisation: loess print-tip
- between arrays normalisation: scale
- least squares (for linear model) in limmaGUI (default in limma)

Thanks for your help,

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK