Entering edit mode
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@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")
