[BioC] affymtrix transcript_cluster categories

[Joao Sollari Lopes]

Hi,

I am using Zebrafish Gene 1.1 ST Array Strip from Affymetrix. Affymetrix 
categorizes the transcript clusters as:

main - part of the main design
control->affx - a standard AFFX control
control->chip - a chip control
control->bgp->antigenomic - contains antigenomic background probes
control->bgp->genomic - contains genomic background probes
normgene->exon - from an exonic region of a normalization control gene
normgene->intron - from an intronic region of a normalization control gene
rescue - contains probes tiled across an mRNA transcript which either 
did not align to the genome, or aligned poorly

I was wondering if it makes sense to use the "rescue" transcript 
clusters when searching for differentially expressed genes.

Sorry that this question is not directly related to bioconductor, but I 
am not sure where to ask for this (I tried Affymetrix las month, but 
still haven't got an answer)

Best,
Joao Lopes
Instituto Gulbenkian de Ciencia