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="sample_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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