[BioC] comparing hgu133a chips with 3mg total RNA to 1mg total RNA

Rafael A. Irizarry ririzarr at jhsph.edu
Tue Sep 30 01:08:40 MEST 2003

one would hope that bolstad's quantile normalization would make them
comparable. gcrma uses this normalization by default. but in my opinion
one can only answer this question with data.

On Mon, 29 Sep 2003, Dick Beyer wrote:

> Would anyone have experience or opinions about comparing hgu133a chips with a starting amount of 3mg total RNA to some chips with a starting amount of 1mg total RNA?  I have a 12 chip experiment, but two of the chips have the lower starting total RNA.  
> Visually, the two lower RNA chips are quite distinctive in comparing boxplots for the raw data, but the gcrma results look quite comparable.
> This brings up a more general question of how much can the starting total RNA for these types of arrays vary and still be compared using gcrma?
> Thanks for any ideas or suggestions,
> Dick
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> Richard P. Beyer, Ph.D.	University of Washington
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