[BioC] replicates and low expression levels

Crispin Miller CMiller at picr.man.ac.uk
Fri May 30 18:28:45 MEST 2003


Hi,
Just a quick question about low expression levels on Affy systems - I hope it's not too off-topic; it is about normalisation and data analysis...
I've heard a lot of people advocating that it's a good idea to perform an initial filtering on either Present Marginal or Absent calls, or on gene-expression levels (so that only genes with an expression > 40, say, after scaling to a TGT of 100 using the MAS5.0 algorithm, are part of the further analysis). Firstly, am I right in thinking that this is to eliminate data that are too close to the background noise level of the system.

I wanted to canvas opinion as to whether people feel we need to do this if we have replicates and are using statistical tests - rather than just fold-changes - to identify 'interesting' genes. Does the statistical testing do this job for us?

Crispin
 
--------------------------------------------------------

 
This email is confidential and intended solely for the use of th... {{dropped}}



More information about the Bioconductor mailing list