Hi Mikhail, Mikhail Spivakov wrote: > Hello everyone, > > I'm reading affy data using ReadAffy and have just noticed that the total > number of probes listed in the intensity table is about 10k larger than the > number of probes associated with probesets - at least as returned by > indexProbes (see example below). I'm wondering if this is how it is supposed > to be - and if so, whether these "orphan" probes are used in any way by any > standard analysis procedures? The short answers are 'yes' and 'no'. If you look closely at an image of an affy chip you can see that there are a bunch of probes around the perimeter that alternate from bright to dark. These are used for instrument alignment when the chip is scanned. There are also some that are used to tile down the chip name as well as some in the center of the chip as well. You can see these by zooming in on the top left corner. Using the Dilution dataset in affydata: library(affy) library(affydata) data(Dilution) a <- exprs(Dilution[,1]) a <- as.matrix(rev(as.data.frame(matrix(a, 640, 640)))) image(1:100, 1:100, log(a[1:100, 541:640]), col = gray(c(0:64)/64)) Since these probes are only used for alignment, they are ignored by all further processing of the data. Best, Jim > > esExpDesc <- read.AnnotatedDataFrame("experimentDescription.txt", esPath, > header=TRUE, sep = "\t", stringsAsFactors = TRUE, row.names=1) > esAffyExp <- ReadAffy(filenames = rownames(pData(esExpDesc)), phenoData = > esExpDesc, celfile.path = esPath, verbose = TRUE) > nrow(exprs(esAffyExp)) > #[1] 1004004 > length(unlist(indexProbes(esAffyExp, which="both"))) > #[1] 992936 > > Many thanks > Mikhail > > == > Mikhail Spivakov PhD > European Bioinformatics Institute > Hinxton > UK > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- 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

Jim, thanks very much for explaning! Best wishes, Mikhail On 2/1/10, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Mikhail, > > Mikhail Spivakov wrote: >> Hello everyone, >> >> I'm reading affy data using ReadAffy and have just noticed that the total >> number of probes listed in the intensity table is about 10k larger than >> the >> number of probes associated with probesets - at least as returned by >> indexProbes (see example below). I'm wondering if this is how it is >> supposed >> to be - and if so, whether these "orphan" probes are used in any way by >> any >> standard analysis procedures? > > The short answers are 'yes' and 'no'. > > If you look closely at an image of an affy chip you can see that there > are a bunch of probes around the perimeter that alternate from bright to > dark. These are used for instrument alignment when the chip is scanned. > > There are also some that are used to tile down the chip name as well as > some in the center of the chip as well. You can see these by zooming in > on the top left corner. Using the Dilution dataset in affydata: > > library(affy) > library(affydata) > data(Dilution) > a <- exprs(Dilution[,1]) > a <- as.matrix(rev(as.data.frame(matrix(a, 640, 640)))) > image(1:100, 1:100, log(a[1:100, 541:640]), col = gray(c(0:64)/64)) > > Since these probes are only used for alignment, they are ignored by all > further processing of the data. > > Best, > > Jim > > > > >> >> esExpDesc <- read.AnnotatedDataFrame("experimentDescription.txt", esPath, >> header=TRUE, sep = "\t", stringsAsFactors = TRUE, row.names=1) >> esAffyExp <- ReadAffy(filenames = rownames(pData(esExpDesc)), phenoData = >> esExpDesc, celfile.path = esPath, verbose = TRUE) >> nrow(exprs(esAffyExp)) >> #[1] 1004004 >> length(unlist(indexProbes(esAffyExp, which="both"))) >> #[1] 992936 >> >> Many thanks >> Mikhail >> >> == >> Mikhail Spivakov PhD >> European Bioinformatics Institute >> Hinxton >> UK >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > -- > 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 > > -- Sent from my mobile device