[BioC] rma and brightness of exon arrays

[Rob Dunne]

Hi,

I am using rma to normalize a set of Affymetrix exon 1.0 ST arrays. I have done
this both with the oligo package and with the Affymetrix Power Tools to get
equivalent results. 

I find that the first principal component is completely determined by one of the
quality measures, namely pos_control_mean (the mean of the positive control
probes as returned by Affymetrix Power Tools) to the extent that pos_control_mean
and PCA 1 have an R^2 of 0.93.

There is no sign of any outliers. It appears to me that the rma normalization is
not removing the brightness effect at all. 

I find this surprising. Is this what other people are seeing? 

I am regressing the normalized data on the pos_control_mean and doing further
analysis on the residuals.

Bye
R