Affymetrix - index of probes
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@benjamin-haibe-kains-955
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@benjamin-haibe-kains-955
Last seen 9.6 years ago
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. However, we can see in the Affymetrix doument http://www.affymetrix.com/support/technical/datasheets/human_datasheet .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
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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_datashe et.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 ... > -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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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
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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
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> 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? Which version of tkWidgets are you using? Do you have DynDoc installed?
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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 ... >> > >
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