[BioC] stats on probes instead of summary values?

Ben Bolstad bolstad at stat.berkeley.edu
Wed Dec 17 18:13:34 MET 2003

I am currently preparing a manuscript discussing this issue in relation
to the RMA model (or variants of).  Some of this implemented in the
affyPLM package.

I am a little perplexed by your statement that RMA only considers probes
from individual chips. Perhaps, you need to take a closer look at the


On Wed, 2003-12-17 at 09:03, Jenny Drnevich wrote:
> Hello all,
> I have been following the recent exchanges Re: ttest or fold change with a 
> lot of interest, particularly the limitations of small sample sizes (i.e., 
> 3 chips per treatment). The question I would like to raise is that for Affy 
> chips, why not use the probe-level values instead of summary values for 
> statistical tests as Chu, Weir & Wolfinger (2002, Math. Biosci. 176:35-51) 
> suggest? It seems like you throw away a lot of power to detect differences 
> when you summarize 14 or 20 PM probes into one summary value. I In fact, 
> the median polish used by RMA to summarize is a linear additive model 
> somewhat similar to the mixed model used by Chu et al.; RMA only considers 
> the probes from one chip, while Chu et al's uses the probes from all chips, 
> along with cell line, treatment, and interaction effects (I still use the 
> gcrma background correction and normalization on PM values). I'm not 
> suggesting that this is a good substitute for conducting more replicates 
> (I, too, am from a behavioral ecology background and tend to think an 
> adequate sample size is at least 15-20), but I think it is a way to get 
> more accurate information on differential expression from only a few 
> replicates. I would like to get your thoughts on whether this is or isn't a 
> valid method for analysis and why.
> Thanks,
> Jenny
> Jenny Drnevich, Ph.D.
> Department of Animal Biology
> University of Illinois
> 515 Morrill Hall
> 505 S Goodwin Ave
> Urbana, IL 61801
> ph: 217-244-6826
> fax: 217-244-4565
> e-mail: drnevich at uiuc.edu
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