[BioC] LIMMA: Technical replication (dye swap) and within-array replicate spots

[Pie Muller]

Dear Gordon,

I am analysing a simple two-colour microarray experiment camparing strain A 
vs. strain B with 3 biological and two technical replicates (dye swap). 
Hence, my experiment is similar to your example in section 11.1 of the 
limma user's guide. Our array has four within-array replicate spots for 
each gene. As the "block" argument in the limma function "lmFit" must be 
NULL if ndups is larger than 2 I wonder how I can handle both technical and 
within-array replicates?

In advance, many thanks for any suggestions!

Pie




_______________________________________________________

Dr Pie Mueller

Vector Research Division
Liverpool School of Tropical Medicine
Pembroke Place
Liverpool
L3 5QA
UK

Tel. +44 (0)151 705 3123 (office)
Tel. +44 (0)151 705 3140 (Gwen Finnegan Dept Secretary)
Fax. +44 (0)151 705 3369