[BioC] alternative CDF (Tarca, Adi)

[rcaloger]

You can find alternative CDF related to the paper of Dai et al. NAR 2005 at:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
I have used them and in my personal experience the RefSeq remapping 
works better than Entrez Genes remapping.
 In our hands some qPCR validated probe sets based on Affy probesets are 
lost using the Entrez Genes (EG) based custom CDFs. Furhtermore, 
comparing fold changes between the same subset of genes identified using 
Affy probesets or EG based probesets a generalized reduction of  fold 
change range was observed.
Best
Raffaele

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Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705420
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   www.bioinformatica.unito.it