[BioC] Application of PAMR from Affy to spot data

Tan, MinHan MinHan.Tan at vai.org
Tue Sep 28 07:04:00 CEST 2004


Good morning,
 
Sorry for the trouble.

I am trying to apply a pamr gene classifier obtained from Affymetrix
data onto spot cDNA array data. For the Affy data, we have tumors , as
well as several normals. The spot cDNA data is tumor against normal. 
 
I was hoping that I could get the small gene classifier, somehow (black
box) modify this classifier with the mean value of the corresponding
gene from normal tissue, and apply this with pamr.predict onto the spot
data. 
 
I don't really know what Gaussian linear discrimination is, so I am a
little lost in the original paper, but it seems that I should be
modifying the discriminant scores somehow to construct estimates of the
class probabilities.
 
I tried running pamr with all Affymetrix data converted to ratios.
Results are definitely not as good as just using the rma expression
values, which is my preferred option. 
 
I would appreciate any insights on this problem. Thank you!

Min-Han

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