[BioC] Affymetrix Mogene 1 0 ST

[Al Ivens]

Hi all,

I am analysing some Affy mogene-1_0-st-v1 arrays, and have noted that in
their latest annotation resource file for these arrays: 
http://www.affymetrix.com/Auth/analysis/downloads/na27/wtgene/MoGene-1_0
-st-v1.na27.mm9.transcript.csv.zip

there is a column called "category", which is summarised below:

>summary(affy_annotation$category)
            control->affx 
                       22 
control->bgp->antigenomic 
                       45 
                     main 
                    28815 
           normgene->exon 
                     1324 
         normgene->intron 
                     5222 
 rescue->FLmRNA->unmapped 
                       91

The "normgene->exon" loci are annotated as "positive controls", whilst
the "normgene->intron" are annotated as "negative controls".  I have
searched the Affy www site for information on the positive controls
might be, but the best I have managed so far is "from an exonic region
of a normalization control gene".  

I have two questions:
1) Has anyone else had more success in tracking done more info on these
loci (other than getting the sequences and blasting them)?  I am
guessing that they might be for spike-ins, but have not seen anything to
confirm this.

2) Out of curiousity, I was wondering whether the positive controls
could be used for normalisation, but could not find a way of doing it
(i.e. as part of rma).  I am used to controlspots=xyx for two-colour
arrays (normalizeWithinArrays), but have no experience in trying to
apply the same approach to Affy data

Any thoughts/suggestions/guidance greatly appreciated.

Best festive wishes to you all,

a