[BioC] affyQCReport before and after normalization

[James W. MacDonald]

Hi Sebastien,

Running affyQCReport() on an ExpressionSet doesn't really make any 
sense. Probably 2/3 of the quality metrics are directed towards looking 
at the raw data (probe-level), and the other 1/3 uses either residuals 
from fitPLM() or ratios of the expression values.

In other words, affyQCReport() already does quality assessment of both 
pre and post normalized (and summarized) data. Trying to do the 
probe-level quality metrics on expression values doesn't make sense 
since you no longer have probe-level data. In addition, rma() doesn't 
return residuals, so you won't be able to do the boxplot of residuals. 
Really the only thing you would be able to do would be the RLE() plot, 
and that is already done by affyQCReport().

Best,

Jim



Sebastien Gerega wrote:
> Hi,
> I would like to generate affyQCReports for before and after 
> normalization of data. I can obviously generate a QCReport for an 
> affyBatch object quite simply but once I have processed the affyBatch 
> object as follows:
> eset <- rma(affyBatch)
> I am unsure about how to get a second QCReport. The rma process would 
> have normalized and background corrected the affyBatch object to create 
> the exprsSet but how can I access this normalized data to create another 
> QCReport?
> any help would be greatly appreciated. thanks,
> Sebastien
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
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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