[BioC] Summary Statistics

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 11 21:10:39 CET 2005

Hrishikesh Deshmukh wrote:
> Hi All,
> Is is possible to do summary statistics on individual
> CEL files?! How does one accept or reject a CEL file
> (from replicates) for further study?

I use two criteria for rejecting celfiles. First, I look at the plot of 
the PM distributions. If you are using RMA, any chip that is 'too far' 
from the others in a set will usually not work well. Unfortunately, it 
is difficult to quantify what 'too far' really is. If there appears to 
be an outlier, I follow up with a look at the residuals from the 
medianpolish fit (using rmaPLM() and image(Pset, type = "resid") from 
the affyPLM package). Again, this is an eyeballometric call on my part. 
If the possible outlier appears to have much larger outliers on the 
residual plot, I either reject it or we re-fragment and re-hyb the sample.



> Thanks,
> Hrishi
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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