Thanks James. That works perfect for me. And as you rightly said I would need to tinker things by hand for the QC Report and viewing the intensity of a probe across arrays. For QC Report I tried qc.data <- qc(celData) and got the following message: Error in setQCEnvironment(cdfn) : Could not find array definition file ' hugene10stv1.r3cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. Any pointers on where I could find some information to try things by hand? Thanks for your time and help. Regards Arun A K Graduate Student Department of Computer Science Indiana University, Bloomington On Tue, Mar 30, 2010 at 10:53 AM, James MacDonald <jmacdon@med.umich.edu>wrote: > Hi Arun, > > Try > > celData <- ReadAffy(cdfname = "hugene10stv1.r3cdf") > > Also note that much of the functionality of simpleaffy (and possibly > affyQCReport) are predicated on the chip having MM probes, which the HuGene > chip does not, so you will be better off doing things by hand. > > Best, > > Jim > > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > >>> Arun A K 03/29/10 11:01 AM >>> > Hi > > I tried the following steps: > > biocLite("hgu133plus2cdf") > > library(affy) > library(simpleaffy) > library(affyQCReport) > setwd("/temp/Cel-Data") > celData <- ReadAffy() > sampleNames(celData) > hist(celData) > > I get the following error when I try hist(celData): > > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > > I looked up for the missing package i.e. hugene10stv1cdf at > http://www.bioconductor.org/packages/release/data/annotation/ and the > closest I could find was > > http://www.bioconductor.org/packages/release/data/annotation/html/hu gene10stv1.r3cdf.html > , > which I installed. But I still get the error. > > I am new to R so I might have done some thing naive. Please let me know > where I have gone wrong. > > Thanks for your time. > > Arun A K > Graduate Student > Department of Computer Science > Indiana University, Bloomington > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]