[BioC] commands of affy and moderated t statistics in experiments

[David Kipling]

Hi

> I have experiments on 1  normal tissue(the 1 normal tissue pooled from
> 8 individual  tissues )  and 12 individual tumor tissues using
> Affymetrix HG-U133A genechips. no replicates. I plan to pre-process the .cel
> files using RMA and do data analysis with moderated t statistics of Limma
> package.

Can I ask what question you are asking biologically/clinically?   Do you
want genes that vary between normal and tumour samples, or genes that vary
amongst your tumour samples (and might therefore be a useful starting point
for some sort of classification study)?

If you are going to do the first then you have a big problem - with only one
'normal' chip you have no idea just how variable any particular gene will be
amongst a population of normal individuals.

Regards

Professor David Kipling
Department of Pathology
School of Medicine
Cardiff University
Heath Park
Cardiff CF14 4XN

Tel:    +44 29 2074 4847
Fax:    +44 29 2074 4276
Email:  KiplingD at cardiff.ac.uk