[BioC] Advice for analyzing Affy data

[Tan, MinHan]

Good evening,

I'm new to R and Affymetrix data analysis. I'd truly appreciate it if
someone could give me some pointers as to how to proceed. I really am
not sure what I'm doing wrong.

(a) performed the ReadAffy() steps, and created expression sets of my
data in both MAS5 (esetmas) and RMA format. (the magnitude difference is
quite startling)

(b) Used genefilter to perform some simple filtering. 
f1<-kOverA(4,150)
ffun<-filterfun(f1)
whichmas<-genefilter(exprs(esetmas),ffun)
exprData <- exprs(esetmas)
filterData <- exprData[whichmas,]

(c) I'm not sure how to perform the ideal form of unsupervised
clustering and how best to view those results as plots.

hc<-hclust(dist(filterData),"ave")
Plot(hc)

All I see is some very skewed looking data, with lots of the AFFX genes
still present. I've tried running the GeneSOM function, but I don't
quite understand the output.

Thank you!!

Best regards,

Min-Han Tan, MD, MRCP(UK)
Laboratory of Cancer Genetics
Van Andel Research Institute
333 Bostwick NE
Grand Rapids MI 49503
Tel: (616) 234-5350
Fax: (616) 234-5115
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message.  Thank you.