Dear all, I am a 1st year Ph.D. student at the University of Bristol and I am working on Microarray data analysis. I downloaded bioconductor to obtain PM and MM probe data from an experiment but when I write > library(affy) > s<-ReadAffy("N1dat.CEL") > s ### to see the data the result is: Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment specified did not contain RAE230A Library - package rae230acdf not installed ###RAE230A is the probe array type Data for package affy did not contain RAE230A Bioconductor - rae230acdf not available AffyBatch object size of arrays=602x602 features (2834 kb) cdf=RAE230A (??? affyids) number of samples=1 Warning message: missing cdf environment ! in: show(structure(list(), exprs = structure(c(202.5, 18912.8, 292.5, Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment specified did not contain RAE230A Library - package rae230acdf not installed Data for package affy did not contain RAE230A Bioconductor - rae230acdf not available I downloaded manually the RAEacdf, RAE annotation and RAE probe package but the same problem persists (exactly the above message appears again). Do you know what should I do? Regards, Makis Motakis ---------------------- E Motakis, Mathematics E.Motakis@bristol.ac.uk

> Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment specified did not contain RAE230A > Library - package rae230acdf not installed > Data for package affy did not contain RAE230A > Bioconductor - rae230acdf not available > > I downloaded manually the RAEacdf, RAE annotation and RAE probe package but > the same problem persists (exactly the above message appears again). Do you > know what should I do? Hi Makis, You need to install the RAE230Acdf package (the probe and annotation packages are not necessary, but they are useful, so may as well install those too) before affy will recognise your CEL files. Cheers, Ken