SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?
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@stephen-piccolo-6761
Last seen 3.5 years ago
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Hi Andrew, Thanks for your email! The normalization process in SCAN is done at the probe level. This is executed in the same way, behind the scenes, regardless of whether a probeSummaryPackage is specified. Thus at the probe level, the results should be identical either way. However, the values that are returned by the SCAN function are summarized at the probeset or gene level. When you use the probeSummaryPackage option (such as when you're using BrainArray annotations), it will do two things: 1) use a subset of probes as defined in the annotations and 2) map the probes to gene IDs rather than Affymetrix-defined probesets. One of the great things about SCAN is that you can also get the underlying (normalized) probe values and do whatever you want with them (e.g., apply JetSet). To do this, specify a value for the probeLevelOutDirPath parameter. This will create an output file in the specified directory that contains the X-Y position and value for each probe. Please let us know if any of your questions weren't answered. Regards, -Steve ---------------------------------------------------------------------- ----- ---------------------------- Stephen Piccolo, Ph.D. Postdoctoral Research Associate @stevepiccolo Affiliations: Department of Pharmacology and Toxicology, University of Utah Computational Biomedicine Section, Boston University School of Medicine ---------------------------------------------------------------------- ----- ---------------------------- From: Andrew Yates <yates.115@osu.edu> Date: Tuesday, May 14, 2013 2:16 PM To: Stephen Piccolo <stephen.piccolo at="" hsc.utah.edu=""> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs? 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/e ntrezg.asp [2] http://www.cbs.dtu.dk/biotools/jetset/ <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 at="" osu.edu=""> wrote: It does, thank you. On Mon, Mar 4, 2013 at 1:39 PM, Steve Piccolo <stephen.piccolo at="" 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 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 <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")
Normalization hgu133a probe affy PROcess SCAN.UPC Normalization hgu133a probe affy • 1.5k views
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Andrew Yates ▴ 20
@andrew-yates-5803
Last seen 9.6 years ago
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") >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > [[alternative HTML version deleted]]
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