[BioC] GC-RMA - interpretation of the expression levels

[Pintilie, Melania]

Hello everyone,

I am a statistician at the Ontario Cancer Institute. Recently, I had to
analyse an affymetrix dataset. The data have been normalized and the level
expressions were calculated using GC RMA as implemented in R.
My role is to analyse the expression levels (which were calculated using GC
RMA) using SAM and other statistical techniques.
The expression levels which were given to me (calculated with GC RMA) are
very large: all are >1. I wonder if this is what one would expect. The
analyst assures me that a log transformation was also applied.

I am not sure how to interpret this numbers. What would be the levels of:
'not expressed', 'over expressed', or 'under expressed'?

For example I know that the expression levels (not logged) obtained using
cDNA microarray can be interpreted (ideally)as: 1=no expression, >2 over
expression and <0.5 under expression.

I appreciate your help.
Thank you.


Melania Pintilie
Biostatistics Department
Ontario Cancer Institute
University of Health Network/Princess Margaret Hospital
Toronto, M5G 2M9
Canada
Tel: (416) 946-4501 ext. 4886
Fax: (416) 946-2048