[BioC] Microarray pattern standardization and fold change cut-offs

[Johan van Heerden]

Dear all,

I have a burning question wrt the use of gene expression pattern standardization (i.e. subtracting mean or meadian and dividing by SD) as is commonly done prior to clustering.

During gene selection steps I typically use a fold-change cut off on a list of differentially expressed genes to further enrich the list for candidate genes with larger fold changes. I have noticed a very strong positive correlation between fold-change and variance (i.e. genes with a big fold change have big variances). However, when I plot the fold changes of standardized patterns, the correlation between fold-change and variance has obviosuly been elimated. I was wondering if a fold-change filter would still be meaningful once the patterns have been standardized and if not what would the reasons for this be (i.e. why is it not meaningful anymore)?

Any feedback is much appreciated!

Sincerely,
Johan
Department of Molecular and Cell Biology
University of Cape Town
South Africa