[BioC] Normalizing by Within Condition - a bad idea

[Naomi Altman]

The question of whether normalizing by condition is reasonable 
frequently comes up on this list.  For a recent talk, I took the 
first 2 conditions (experiments) of the Affymetrix Latin Square 
spikein experiment and normalized by RMA all together and within 
treatment.  The experiment uses identical RNA except for 42 spike-ins 
which are varied by condition.  There are 3 replicates, making 6 arrays in all.

The number of "significant" genes at p<.01 using limma with eBayes 
(but no multiple comparison adjustment) is 144 (capturing most but 
not all of the spike-ins) when the arrays are normalized together and 
14374 when they are normalized by experiment.


Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111