[BioC] limma help - choosing an approach

Gaj Stan (BIGCAT) Stan.Gaj at BIGCAT.unimaas.nl
Tue Sep 19 09:17:31 CEST 2006

Dear Gordon and rest,

I've been following the outcome of this thread carefully and am persuing
a single-channel analysis for a couple of Agilent arrays as well. Do you
(or anyone else for that matter) happen to know if there are any
publications available that implemented or have tested this approach?

Best wishes,


PhD Student
Dept. of Human Biology & BiGCaT Bioinformatics
PO BOX 616
UNS 40 Room 5.578
6200 MD Maastricht
Tel: +31 (0) 433882913

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon
Sent: 15 September 2006 06:09
To: BioC Mailing List
Subject: [BioC] limma help - choosing an approach

Dear John,

I wrote the warning in the ?lmscFit documentation about it being 
somewhat experimental more than two and a half years ago, when the 
function were first introduced into the limma package. I've done much 
more testing since then, and the function has stood the test of time, 
so I'll remove the warning.

Best wishes

>[BioC] limma help - choosing an approach
>john seers (IFR) john.seers at bbsrc.ac.uk
>Thu Sep 14 12:19:39 CEST 2006
>Hello Naomi (and anyone else)
>Thanks again for your help. It has  been extremely helpful. Almost
>I think, though I am still just doing it on autopilot and not quite
>how meaningful this is. I am slightly worried by the limma
>which describes the single channel analysis as "experimental" so
>combined with my lack of understanding makes me feel quite uncertain.
>Anyway I can run it now and pull out lists of genes - though what they
>mean I am not sure yet.

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