Hi Bioconductor mailing list and Dr. Stephen Piccolo,

In SCAN.UPC, does the application of a custom probe summary package like
Brainarray[1] substantially change the normalized value per probe, or does
it merely return a subset of results? That is, what is the difference,
besides the number of probes returned, between "M.brainarray.SCAN" and
"M.all.SCAN" below?

Further, is it acceptable to apply SCAN.UPC with no probeSummaryPackage
parameter and then select representative probes using a package like
JetSet[2] afterwards?

Best,
Andrew

[1]
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.asp
[2] http://www.cbs.dtu.dk/biotools/jetset/

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

M.brainarray.SCAN = SCAN(my.path.to.cels,
probeSummaryPackage=hgu133ahsentrezgprobe)

M.all.SCAN = SCAN(my.path.to.cels)


On Mon, Mar 4, 2013 at 4:50 PM, Andrew Yates <yates.115@osu.edu> wrote:

> It does, thank you.
>
>
> On Mon, Mar 4, 2013 at 1:39 PM, Steve Piccolo <
> stephen.piccolo@hsc.utah.edu> wrote:
>
>> 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@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<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.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")
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

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