I am using the gcrma package in R to analyze affymetrix HGu133A chips and would like to normalize only the probes called present by GCOS. I can separate the probes called present from the rest by using the chp file exported to excel, however, I would need to recreate it as a .cel file for use in R. Is it possible to do this? Is it possible to use an excel file in R, rather than a .cel file? Any suggestions? Any help would be much appreciated. Thanks, Josh

Hi Josh, Not sure whether anyone has responded to your mail yet, but I think an easier way to do this would be to load your data in, normalise it then calculate detection calls (present/absent calls) and then use these to filter only out those probesets called present.. library(simpleaffy) library(gcrma) # read in all the cel files in the current directory raw.data <- ReadAffy() # normalise using gcrma gcrma.eset <- call.exprs(raw.data, "gcrma") # calculate detection calls # present/absent calls are stored in the $call slot calls.eset <- detection.p.val(raw.data) # show the complete present/absent calls table for the expression set, # columns are different chips, rows are the probesets calls.eset$call # summarise the calls for filtering # effectively counts how many times a particular probeset is called present calls.sum <- rowSums(calls.eset$call == "P") # to get all probesets that are present on all chips present.all.chips <- names(calls.sum[calls.sum==length(colnames(gcrma.eset at exprs))]) # filter your expression levels # to retrieve expression levels of only those probesets called present on all chips filtered.set <- gcrma.eset at exprs[present.all.chips,] # to get all probesets that are present on x chips # make x equal to minimum number of times a probeset must be called present present.some.chips <- names(calls.sum[calls.sum==x]) hope this helps/makes sense! claire > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Garcia, Joshua A > Sent: 15 July 2005 16:35 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] filtering for present calls > > I am using the gcrma package in R to analyze affymetrix > HGu133A chips and > would like to normalize only the probes called present by > GCOS. I can > separate the probes called present from the rest by using the > chp file > exported to excel, however, I would need to recreate it as a > .cel file for use > in R. Is it possible to do this? Is it possible to use an > excel file in R, > rather than a .cel file? Any suggestions? Any help would be much > appreciated. > > Thanks, > Josh > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}