Re: how to rank affy probesets by their probe-effect magnitude

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>package.
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/RPA/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@...>
To: Bioconductor mailing list <bioconductor@...>
Subject: [BioC] how to rank affy probesets by their probe-effect
       magnitude
Message-ID: <1330971744.2703.40.camel@...>
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.

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