Hi Rich,
Please check out the aroma.affymetrix package and their very helpful
website here:
http://www.aroma-project.org/
It is a very powerful package, and I think a little bit of overkill
for ST arrays, but that is the only way I have found to get the plots
you are looking for (not that I have looked that hard for other
packages that could do it).
When using the aroma.affymetrix package, you have to be very specific
in how the data files (and folders) are named and structured, which is
all documented on their web site. Once you do that, you can fit an RMA
probe-level (PLM) model, and then do something like this:
#################################################################
### Quality assessment of PLM fit
#################################################################
#To examine NUSE and RLE plots, do
brca.qam <- QualityAssessmentModel(brca.plm)
par(mfrow=c(1,2))
plotNuse(brca.qam)
plotRle(brca.qam)
If you want some additional QC plots, you can also use the
affyQCReport package. It doesn't work entirely because some of its
functions aren't defined for ST arrays (no mismatch probes), but you
can get most of the plots that are generated by QCReport() using the
following code (note this is for a different data set than used
above). Getting the annotation correct is the only slightly tricky
part. Here I was using Mouse ST 1.0 array.
library(affy)
library(geneplotter)
library(simpleaffy)
library(limma)
library(statmod)
library(lattice)
library(mogene10sttranscriptcluster.db)
MEF.eSet <- ReadAffy(phenoData=read.AnnotatedDataFrame(filename="sampl
e_info.csv",sep = ","))
annotation(MEF.eSet) = "mogene10sttranscriptcluster.db"
###################################################
### Quality Control
###################################################
#Used Aroma.affymetrix for NUSE and RLE plot, they looked fine.
#affyQC Report doesn't work well with ST arrays
library(affyQCReport)
#QCReport(MEF.eSet,file="MEF_PreProc_QC2.pdf")
## Read this entire thread about QCReport and ST
##
http://thread.gmane.org/gmane.science.biology.informatics.conductor/
32460/focus=32815
#However, this does everything but the degradation plot
pdf("myownQC.pdf")
borderQC1(MEF.eSet)
borderQC2(MEF.eSet)
correlationPlot(MEF.eSet)
titlePage(MEF.eSet)
signalDist(MEF.eSet)
MEF.norm <- expresso(MEF.eSet,
bgcorrect.method="rma",
normalize.method="quantiles",#normalize.method="qspline",
pmcorrect.method="pmonly",
summary.method="medianpolish")
library(affycoretools)
#par(mfrow=c(2,1))
plotHist(MEF.eSet) # prior to any normalization, etc
plotDeg(MEF.eSet)
dev.off()
HTH,
Wade
J. Wade Davis, PhD
Assistant Professor
187 Galena DC 018.0
University of Missouri
Columbia, MO 65212
Phone: (573) 882-0770
Fax: (573) 884-4196
MU Biostatistics Group
-----Original Message-----
From: Richard Friedman [mailto:friedman@cancercenter.columbia.edu]
Sent: Thursday, February 03, 2011 5:46 PM
To: Bioconductor mailing list
Subject: [BioC] st 1.0 gene quality measures
Dear Bioconductor List,
Is there a way to get quality measurements on ST 1.0 Gene Arrays
analogous to the standard
workup for mouse 430?
That is to say plm functions (NUSE, signed resids etc).
unnormlaizd boxplots and rma normlaized boxplots.
pca , hist
It is not clear to me how to do this from the documentation to
the
oligo pacakage.
I would greatly appreciate any suggestions that you might have.
Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
"Did he win the Nobel prize or the Ig Nobel
prize for levitating the frog?".
Rose Friedman, age 14
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