[BioC] Defining and handling replicates

[Gordon K Smyth]

> Date: Thu, 02 Jun 2005 09:18:01 +1000
> From: Jonathan Arthur <jarthur at med.usyd.edu.au>
> Subject: [BioC] Defining and handling replicates
> To: bioconductor at stat.math.ethz.ch
>
> Hello,
>
> I am using Affymetrix arrays to compare two groups of samples (5 in one
> group and 4 in the other). I have been using affy, affylmGUI, and limma
> for the analysis. Some of the samples in the latter group have
> replicates and I'd like to know how to handle these. My questions are:

Have you read the sections on technical replication in the Limma User's Guide?  That would be the
place to start.

> 1) In one case, the replicate is drawn from the same sample but at a
> later time point. Is this a technical replicate (because it is the same
> sample but different chip), biological replicate (i.e., the different
> time point make it *effectively* a different sample), or neither (and
> thus can't be used)?

Does "drawn at a later time point" mean that the RNA was extracted from the same organisim but at
a later time?  Or does it mean that the RNA was simply aliquoted later from a stored sample?  You
would need to describe your experiment much more fully before people could help you with the
analysis.

> 2) I assume I need to average the gene expression of the technical
> replicates before doing the analysis and treatment them as *one* sample?
> Is this correct?

Last resort.

Gordon

> 3) Assuming I do need to average the expression of the technical
> replicates, are there methods in affy or limma to do this? Or do I need
> to do it manually with something like:
>
> Data <- ReadAffy()
> eset <- rma(Data)
> # do something here to create a new eset where the technical replicate
> columns have been replaced by a single column averaging the two
> # go on to limma analysis
>
> Thanks,
>
> Jonathan
>
> --
> Dr Jonathan Arthur
> Sesqui Lecturer in Bioinformatics
> Central Clinical School, Faculty of Medicine and SUBIT
> Medical Foundation Building, K25
> University of Sydney
> Ph: +61 2 9036 3132
> Email: jarthur at med.usyd.edu.au