Thanks a lot ! Affymetrix documentation seems to be not enough precise ... James W. MacDonald wrote: > Benjamin Haibe-Kains wrote: > >> Hi, >> >> I want to compare affy hgu133a and hgu133plus2 chips. When I retrieve >> the index of different probes on these two chips, the function >> indexProbes (see affy package) returns a list of 16 probes for the pm >> and 16 probes for the mm for each probe set. > > > Not exactly true. There are some probesets with greater or less than > 11 PM probes, but in general there are 11 per probeset. > > > cdfName(dat) > [1] "HG-U133A" > > table(unlist(lapply(indexProbes(dat, "pm"), length))) > > 8 10 11 13 14 15 16 20 69 > 1 1 21748 4 4 2 482 40 1 > > > cdfName(dat2) > [1] "HG-U133_Plus_2" > > table(unlist(lapply(indexProbes(dat2, "pm"), length))) > > 8 9 10 11 13 14 15 16 20 69 > 5 1 6 54130 4 4 2 482 40 1 > > HTH, > > Jim > > > >> >> However, we can see in the Affymetrix doument >> http://www.affymetrix.com/support/technical/datasheets/human_datash eet.pdf >> >> that there are only 11 probes per probe set ! I don't understand the >> origin of the 5 exceeded probes ... >> >> Can you help me ? >> >> thanks >> >> NB: this email is maybe duplicated ... >> > > -- Benjamin Haibe-Kains Licence in Computer Science Master in Bioinformatics Free University of Brussels (ULB) E-mail: bhaibeka@ulb.ac.be MicroArray Unity Institute Jules Bordet (IJB) E-mail: benjamin.haibekains@bordet.be

Hi. I'm having a problem with tkWidgets in Bioconductor devel version under R 2.0.0 (Debian testing/unstable). Using vExplorer() or viewVignette() I get an error message as it cannot find the function getVignetteCode. Where is the problem, i.e. why the function is missing? TIA, Stefano

Just a (side) comment. The probe set with 69 probes (see James' very demonstrative example), is an odd one: all its probes are designed to match ALU repeats. The probe set does not monitor the expression level of a particular gene (and computing the expression value for it does not necessarily make a lot of sense). L. James W. MacDonald wrote: > Benjamin Haibe-Kains wrote: > >> Hi, >> >> I want to compare affy hgu133a and hgu133plus2 chips. When I retrieve >> the index of different probes on these two chips, the function >> indexProbes (see affy package) returns a list of 16 probes for the pm >> and 16 probes for the mm for each probe set. > > > Not exactly true. There are some probesets with greater or less than 11 > PM probes, but in general there are 11 per probeset. > > > cdfName(dat) > [1] "HG-U133A" > > table(unlist(lapply(indexProbes(dat, "pm"), length))) > > 8 10 11 13 14 15 16 20 69 > 1 1 21748 4 4 2 482 40 1 > > > cdfName(dat2) > [1] "HG-U133_Plus_2" > > table(unlist(lapply(indexProbes(dat2, "pm"), length))) > > 8 9 10 11 13 14 15 16 20 69 > 5 1 6 54130 4 4 2 482 40 1 > > HTH, > > Jim > > > >> >> However, we can see in the Affymetrix doument >> http://www.affymetrix.com/support/technical/datasheets/human_datash eet.pdf >> >> that there are only 11 probes per probe set ! I don't understand the >> origin of the 5 exceeded probes ... >> >> Can you help me ? >> >> thanks >> >> NB: this email is maybe duplicated ... >> > >