Thanks James, that's exactly what we are looking for. From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> To: Stacy_Xu at bd.com Cc: bioconductor at stat.math.ethz.ch Date: 08/12/2010 02:33 AM Subject: Re: [BioC] Affy ST 1.0 gene chip background probes cut off set up _________________________________________________________________ Hi Stacy, On 8/11/2010 10:51 AM, Stacy_Xu at bd.com wrote: > > Hi, guys > There are several ways to do the background corrections for the new ST 1.0 > chip from Affy from bio-conductor like xps, affy- aroma,pdfInfo and rma. And > almost all of those have a parameter to indicate background correction or > subtraction. According to Affy data sheet for human ST 1.0 array, > "Background is estimated using a set of approximately 17,000 generic > background probes. Standard poly-A controls and hybridization controls are > represented on the arrays to allow convenient troubleshooting along the > entire experimental process." > I am wondering are the information or IDs of those 17,000 background RNA > probes somewhere in the CEL file where I can set up my negative cut off > expression level? They do have some "antigenomic" controls, but there are > only about 60 of those and they are not what we want. Actually, I believe those are what you want (and I count 45 of them). Note that Affy states there are 17k _probes_, not probesets. If you look at the number of probes in a probeset for controls, you will see that they can number in the thousands. For instance, the AFFX-Bs-thr_st control probeset has 1189 probes. And the data for these controls are in the celfile, as they are used by Affy's software. However, the cdf package that we make available for this chip, which is based on the unsupported cdf from Affy, doesn't contain the locations for these probesets. However, the pd.hugene.1.1.st.v1 package that you can use in conjunction with the oligo package does contain these probe locations. As a check, I downloaded the annotation csv file from Affy and grep'ed out the antigenomic probe IDs. I then loaded up the pd.hugene.1.1.st.v1 package and looked to see how many probes there are: > bgp <- read.csv("bgp.csv", header=F) ## csv file with only antigenomic probes > dim(bgp) [1] 45 39 > sql <- paste("select * from pmfeature where fsetid in ('", paste(bgp[,1], collapse = "','"), "');", sep = "") > library(pd.hugene.1.1.st.v1) > con <- db(pd.hugene.1.1.st.v1) > a <- dbGetQuery(con, sql) > nrow(a) [1] 16943 So the 45 antigenomic probesets have just about 17k probes. AFAIK, oligo uses basic RMA to do background correction, so would not use these antigenomic probes. However, you can access them if you are willing to do some work. Best, Jim > Thanks, > Stacy > ******************************************************************* ***** > This message (which includes any attachments) is intended only for the > designated recipient(s). It may contain confidential or proprietary > information and may be subject to the attorney-client privilege or other > confidentiality protections. If you are not a designated recipient, you may > not review, use, copy or distribute this message. If you receive this in > error, please notify the sender by reply e-mail and delete this message. > Thank you. > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > [1]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [2]http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues References 1. https://stat.ethz.ch/mailman/listinfo/bioconductor 2. http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Christian, Thanks very much for the information. Best regards, Stacy From: cstrato <cstrato at="" aon.at=""> To: Stacy_Xu at bd.com Cc: bioconductor at stat.math.ethz.ch Date: 08/12/2010 05:25 AM Subject: Re: [BioC] Affy ST 1.0 gene chip background probes cut off set up _________________________________________________________________ Dear Stacy, Since you mention xps, it may be of interest to you that xps supports four background algorithms: - rma background - sector background (mas4) - weigthed sector background (mas5) - gccontent background (see vignette xpsPreprocess.pdf) For the ST 1.0 arrays you can use gccontent background with the generic background probes by setting parameter "bgcorrect.select" either to "genomic" or "antigenomic". Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 8/11/10 4:51 PM, Stacy_Xu at bd.com wrote: > > Hi, guys > There are several ways to do the background corrections for the new ST 1.0 > chip from Affy from bio-conductor like xps, affy- aroma,pdfInfo and rma. And > almost all of those have a parameter to indicate background correction or > subtraction. According to Affy data sheet for human ST 1.0 array, > "Background is estimated using a set of approximately 17,000 generic > background probes. Standard poly-A controls and hybridization controls are > represented on the arrays to allow convenient troubleshooting along the > entire experimental process." > I am wondering are the information or IDs of those 17,000 background RNA > probes somewhere in the CEL file where I can set up my negative cut off > expression level? They do have some "antigenomic" controls, but there are > only about 60 of those and they are not what we want. > Thanks, > Stacy > ******************************************************************* ***** > This message (which includes any attachments) is intended only for the > designated recipient(s). It may contain confidential or proprietary > information and may be subject to the attorney-client privilege or other > confidentiality protections. If you are not a designated recipient, you may > not review, use, copy or distribute this message. If you receive this in > error, please notify the sender by reply e-mail and delete this message. > Thank you. > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > [1]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [2]http://news.gmane.org/gmane.science.biology.informatics.conductor > References 1. https://stat.ethz.ch/mailman/listinfo/bioconductor 2. http://news.gmane.org/gmane.science.biology.informatics.conductor