Dear Robert, Below is an example script for ordering the probes based on the probe effect for the 'Dilution' affybatch using the Bioconductor RPA<http: www.bioconductor.org="" packages="" release="" bioc="" html="" rpa.html="">pa ckage. The Robust Probabilistic Averaging (RPA) model estimates probe-specific affinity and variance terms (with respect to the probeset-level summary estimate). The model was originally developed and used to assess the effect of known probe-level error sources on probe performance in TCBB/IEEE 2011<http: www.computer.org="" portal="" web="" csdl="" doi="" 10.1109="" tcbb.2009.38="">(GC-content, SNPs, probe position, crosshyb). Technical summary of the method is available in the package vignette<http: www.bioconductor.org="" packages="" release="" bioc="" vignettes="" r="" pa="" inst="" doc="" rpa.pdf=""> . with kind regards Leo Lahti, Finland / Netherlands # Probe affinity and variance estimation # (C) Leo Lahti 2012. FreeBSD license. # Install libraries source("http://www.bioconductor.org/biocLite.R") biocLite(c("affy", "affydata", "RPA")) # Load libraries require(affy) require(affydata) require(RPA) # Load example data data(Dilution) # Define the probesets to check sets <- geneNames(Dilution)[1:2] # Robust Probabilistic Averaging model rpa.results <- RPA.pointestimate(Dilution, sets) # Probe affinity effects af <- unlist(lapply(sets, function (set) {rpa.results[[set]]$affinity})) # Probe-specific noise (variance) s2 <- unlist(lapply(sets, function (set) {rpa.results[[set]]$sigma2})) # PM probe indices pmind <- unlist(pmindex(Dilution)[sets]) # Probe effect table df <- data.frame(list(pmindex = pmind, affinity = af, variance = s2)) # Probe effect table ordered by absolute affinity effects df <- df[order(abs(df$affinity), decreasing = TRUE),] # Investigate the output print(head(df)) Date: Mon, 05 Mar 2012 19:22:24 +0100 From: Robert Castelo <robert.castelo@upf.edu> To: Bioconductor mailing list <bioconductor@r-project.org> Subject: [BioC] how to rank affy probesets by their probe-effect magnitude Message-ID: <1330971744.2703.40.camel@llull.imim.es> Content-Type: text/plain; charset="UTF-8" dear list, i'm searching for a way to rank affy probesets from classical 3' affy arrays by their probe effect magnitude. i mean that i would like to know if a probeset is has a larger probe-specific effect than another one. [[alternative HTML version deleted]]