[BioC] LIMMA: Technical replication (dye swap) and within-array replicate spots
pie.muller at liverpool.ac.uk
Thu Sep 15 18:55:23 CEST 2005
Sorry, didn't see that this question has been addressed earlier... Still
what would you suggest? Compute the mean values from the replicate spots on
each array after normalisation and use those for fitting the linear model,
or neglecting the "block" effect of the dye-swap? A similar problem occurs
if one considers separate channel analysis of two-colour data.
What is the best way to create a new MAlist object with means from my
original object containing the values for each replicate spot? To use the
function "aggregate"? Couldn't figure out with my basic R knowledge...
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
In advance, many thanks for any suggestions!
Dr Pie Mueller
Vector Research Division
Liverpool School of Tropical Medicine
Tel. +44 (0)151 705 3123 (office)
Tel. +44 (0)151 705 3140 (Gwen Finnegan Dept Secretary)
Fax. +44 (0)151 705 3369
More information about the Bioconductor