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/huge ne10stv1.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]]

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/huge ne10stv1.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 at 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