Dear Han, >before starting any analysis on Affymetrix arrays is important to evaluate >the arrays quality. >How to evaluate the Affymetrix Genechips image artifacts is ok, ugly or >bad but still reasnable >using using the fitPLM of the affyPLM package? >How to write the scripts? About the package affyPLM, I would recomend: 1.- Read the vignette: affyPLM: Model Based QC Assessment of Affymetrix GeneChips 2.- Go to the Ben Bolstad web page, where you can see useful images of artifacts and "bad" chips: http://www.stat.berkeley.edu/~bolstad/PLMImageGallery/ About the arrays quality, I would recommend to do some quality controls of the Affy package (boxplots, histograms, images of the chip, RNA degradation plots, etc.) HTH Jordi Altirriba

Hi, You may also want to have a look at this: http://bioinf.picr.man.ac.uk/simpleaffy/qcstats.jsp Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Jordi Altirriba Guti?rrez Sent: 03 June 2005 15:59 To: hanweinong@yahoo.com; bioconductor@stat.math.ethz.ch Subject: [BioC] Re: how to evaluate the arrays quality? Dear Han, >before starting any analysis on Affymetrix arrays is important to >evaluate the arrays quality. >How to evaluate the Affymetrix Genechips image artifacts is ok, ugly >or bad but still reasnable >using using the fitPLM of the affyPLM package? >How to write the scripts? About the package affyPLM, I would recomend: 1.- Read the vignette: affyPLM: Model Based QC Assessment of Affymetrix GeneChips 2.- Go to the Ben Bolstad web page, where you can see useful images of artifacts and "bad" chips: http://www.stat.berkeley.edu/~bolstad/PLMImageGallery/ About the arrays quality, I would recommend to do some quality controls of the Affy package (boxplots, histograms, images of the chip, RNA degradation plots, etc.) HTH Jordi Altirriba _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi Also have a look at the simpleaffy package, which has some familiar but useful QC criteria presented in a coherent fashion. My own generic QC pipeline goes something like: require(affy) require(affyPLM) require(simpleaffy) # Input the cel files to an AffyBatch object data1 <- ReadAffy() # simpleaffy QC (scaling factors, 3?/5? ratios etc) qcdat <- qc(data1) plot(qcdat) # Look at the distribution of the PM values boxplot(data1) # Look at some RNA degradation plots deg <- AffyRNAdeg(data1) plotAffyRNAdeg(deg) plot(summaryAffyRNAdeg(deg)[1,]) # Do some probe level modelling Pset <- fitPLM(data1) RLE(Pset) NUSE(Pset) image(Pset, type=?resids?) All this is covered in the affy, affyPLM and simpleaffy vignettes. That being said, RMA and MAS5 are pretty robust against slightly dodgy chips (too bright, too dim, fluff, scratches, etc) but what they can't cope with is duff RNA. RNA degradation will affect different probesets differently because of their relative location to the polyA tail, and no amount of flashy post-image processing or normalisation will rescue that. David R 2.1, BioC 1.6 > Dear Han, > >> before starting any analysis on Affymetrix arrays is important to evaluate >> the arrays quality. >> How to evaluate the Affymetrix Genechips image artifacts is ok, ugly or >> bad but still reasnable >using using the fitPLM of the affyPLM package? > >> How to write the scripts? > > About the package affyPLM, I would recomend: > 1.- Read the vignette: > affyPLM: Model Based QC Assessment of Affymetrix GeneChips > 2.- Go to the Ben Bolstad web page, where you can see useful images of > artifacts and "bad" chips: > http://www.stat.berkeley.edu/~bolstad/PLMImageGallery/ > > About the arrays quality, I would recommend to do some quality controls of > the Affy package (boxplots, histograms, images of the chip, RNA degradation > plots, etc.) > > HTH > > Jordi Altirriba > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Professor David Kipling Department of Pathology School of Medicine Cardiff University Heath Park Cardiff CF14 4XN Tel: +44 29 2074 4847 Fax: +44 29 2074 4276 Email: KiplingD@cardiff.ac.uk