[BioC] SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?

[Steve Piccolo]

Hi Andrew,

Thanks for your email. The results you are seeing are expected.

The goal of the BrainArray mappings is to identify high-quality probes and
to enable mapping of individual probes to genes (rather than Affymetrix
probesets). On HG-U133A, BrainArray indicates that only 12,079 genes have
an adequate number of high-quality probes to generate a reliable
summarized value. Please let me know if that doesn't answer your question.

Regards,
-Stephen



From: Andrew Yates <yates.115 at osu.edu>
Date: Friday, March 1, 2013 10:15 PM
To: Stephen Piccolo <stephen.piccolo at hsc.utah.edu>
Subject: SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?


Hi Dr. Piccolo,
I used SCAN-UPC to normalize arrays generated using the Affy hgu133a
platform using the probe annotations from the Brainarray Database[1]. Of
22,283 features in the platform, the resulting file from SCAN-UPC only had
 12,079. In downstream analysis, the results generated from these features
look good, but...

What accounts for these missing features, and did my selection of the
Brainarray Database have an effect on this? Did I use SCAN-UPC in the
recommended way? My R code is included below.

Best,
Andrew

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/e
ntrezg.asp

library(SCAN.UPC)
library(hgu133ahsentrezgprobe)
library(pd.hg.u133a)

LIU.SCAN = SCAN(fname.ptn, probeSummaryPackage=hgu133ahsentrezgprobe,
outFilePath="LIU.SCAN.txt")
LIU.UPC = UPC(fname.ptn, probeSummaryPackage=hgu133ahsentrezgprobe,
outFilePath="LIU.UPC.txt")