[BioC] Human whole genome Codelink arrays and paired analysis

[Matthew Neville]

Hi,

This is my first post to this forum and I am right at the bottom of  
the learning curve when it comes to R but I have a few initial  
questions.

Does anyone have experience with analysing Codelink arrays in R,  I  
see there is a normalisation program which improves on the Codelink  
software but are there any other considerations I need to take into  
account ?.

Also,  my dataset is based on biopsies from 12 individuals taken at 3  
time points after they start taking a drug so when looking for  
differentially expressed genes my most powerful tests would be  
paired, i.e. paired ttest or repeated measures ANOVA equivalents.   
However, most analyses seem to be unpaired, does anyone have any  
advice?.

many thanks in advance

Matt

Matt Neville D.Phil
Oxlip Group
Oxford Centre for Diabetes,Endocrinology and Metabolism
Churchill Hospital
Old Road
Headington
Oxford
OX3 7LJ
matthew.neville at oxlip.ox.ac.uk
TEL: 01865 857289
FAX: 01865 857217