Ting, Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Tue, 21 Feb 2006, Ting-Yuan Liu wrote: > > Hi Dick, > > This situation is resulted from the inconsistence of Affymetrix Mu11KsubA > CDF file. In this file, I found that Affymetrix confused > "AF027865_1_s_at" and "AF027865_s_at" in "Unit3403_Block1", and Affymetrix > also confused "AF027865_2_s_at" and "af027865_s_at" in "Unit3404_Block1". > > I believe that "AF027865_1_s_at" and "AF027865_2_s_at" should replace > "AF027865_s_at" and "af027865_s_at", respectively, according to the > annotation file Affymetrix provides. > > I will report this bug to Affymetrix and hopefully they will correct this > soon. > > Thanks for this report. > > Sincerely, > Ting > ______________________________________ > Ting-Yuan Liu > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > Seattle, WA, USA > ______________________________________ > > On Mon, 20 Feb 2006, Dick Beyer wrote: > >> I have found one or more affy probeids in Mu11KsubA are missing. A query at the netaffx site shows, for Mu11KsubA, there are these two probes: >> >> AF027865_1_s_at >> AF027865_2_s_at >> >> In my R session, I have >> >>> tmp >> AffyBatch object >> size of arrays=534x534 features (2232 kb) >> cdf=Mu11KsubA (6584 affyids) >> number of samples=1 >> number of genes=6584 >> annotation=mu11ksuba >> >>> grep("AF027865_1_s_at",geneNames(tmp),ignore.case=TRUE) >> numeric(0) >> >> z <- grep("AF027865",geneNames(tmp),ignore.case=TRUE) >>> geneNames(tmp)[z] >> [1] "af027865_s_at" "AF027865_s_at" >> >> So the mu11ksuba metadata is missing the probeids and in their place are two identical probeids. >> >> Is this an error in the mu11ksuba metadata, or are probes that have "_1_" and "_2_" variants in the original platform handled with upper and lower case leading letters? >> >> Thanks much, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >