[BioC] Annalyzing replicates in the Agilent chip 4 x44 with limma

[Gordon Smyth]

Dear Ester,

limma doesn't have a feature to treat just a few probes as 
duplicated. One reason for this omission is that unequal replication 
at the within-array level would play havoc with shrinking the 
variances. I'd just treat them all as independent probes.

Best wishes
Gordon

>Date: Wed, 11 Jul 2007 16:14:54 +0300
>From: Ester Feldmesser <ester.feldmesser at weizmann.ac.il>
>Subject: [BioC] Annalyzing replicates in the Agilent chip 4 x44 with
>         limma
>To: bioconductor at stat.math.ethz.ch
>
>Hi everybody,
>
>The human Agilent chip 4x44 has most of the probes only once, but some
>of then appear in 10 replicates. These replicates are genes and not
>controls.
>I am using the Limma package to analyze them. I would like to define
>these replicates as technical ones and leave the other probes (those
>that appear once) as they are.
>What is the best way to define only part of the spots as replicates?
>
>Thanks for your help
>Esti
>--
>
>Ester Feldmesser, Ph.D.
>Bioinformatics Unit, Department of Biological Services
>Weizmann Institute of Science
>Levine Building, Room 110
>phone: +972-8-934-2614
>email: ester.feldmesser at weizmann.ac.il