dear all, I am puzzling with a quite stupid problem, so don't blame me if the answer is something very simple, please. I am working with the affy HG-U133A probe sequences. both the hgu133aprobe package and the file available in affymetrix.com give 16 probe sequences per each probe set. but I would expect only 11. what is the explanation? thanks in advance for your help..! dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm

Hi Dario, Dario Greco wrote: > dear all, > > I am puzzling with a quite stupid problem, so don't blame me if the > answer is something very simple, please. > > I am working with the affy HG-U133A probe sequences. both the > hgu133aprobe package and the file available in affymetrix.com give 16 > probe sequences per each probe set. > but I would expect only 11. > > what is the explanation? There are many different probeset lengths for any given Affy chip. They just report the most common. > a <- as.data.frame(hgu133aprobe) > b <- as.factor(a[,4]) > table(table(b)) 8 10 11 13 14 15 16 20 69 1 1 21748 4 4 2 482 40 1 So there are 482 probesets that have 16 probes, but the vast majority have 11. HTH, Jim > > thanks in advance for your help..! > > dario > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

I looked at my hgu133a data and it seems most of the probesets have 11 probes but there are some exceptions.I have the table of probeset sizes as 8 10 11 13 14 15 16 20 69 1 1 21765 4 4 2 482 40 1 So don't be surprised if you get 16 probes for some probesets. ------------------------------------------- Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-H2 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://stat.brown.edu/~zwu On Thu, 20 Apr 2006, Dario Greco wrote: > dear all, > > I am puzzling with a quite stupid problem, so don't blame me if the > answer is something very simple, please. > > I am working with the affy HG-U133A probe sequences. both the > hgu133aprobe package and the file available in affymetrix.com give 16 > probe sequences per each probe set. > but I would expect only 11. > > what is the explanation? > > thanks in advance for your help..! > > dario > > -- > > Dario Greco > > Institute of Biotechnology - University of Helsinki > Building Cultivator II > P.O.Box 56 Viikinkaari 4 > FIN-00014 Finland > > Office: +358 9 191 58951 > Fax: +358 9 191 58952 > Mobile: +358 44 023 5780 > > Lab WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/ > > Personal WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >