The problem was solved after upgrading to the newest development version of altcdfenvs (version 1.1-11). However, I found that I need to use envsccdf instead of sccdf to make it work, unlike what is described in the vignettes. Envsccdf <- as(sccdf, "environment") abatch@cdfName <- "sccdf" #boxplot(abatch) does not work abatch@cdfName <- "envsccdf" #boxplot(abatch) works Xiwei -----Original Message----- From: Wu, Xiwei Sent: Thursday, March 24, 2005 10:11 AM To: 'bioconductor@stat.math.ethz.ch' Subject: altcdfenvs error I was trying to build a cdfEnvAffy object from yeast2cdf following the documentation of Alternative CDF environment for 2(or more)-genomes chips. I got the following error. Am I missing sth here? > yeastcdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") > print(yeastcdf) Instance of class CdfEnvAffy: name : yeast2cdf chip-type: yeast2cdf size : 496 x 496 10928 probe set(s) defined. > ids <- geneNames(yeastcdf) > ids.yeast<- scan(file="Y_IDs.txt", what="") Read 5814 items > sccdf <- yeastcdf[ids.yeast] > print(sccdf) Instance of class CdfEnvAffy: name : yeast2cdf-subset chip-type: yeast2cdf size : 496 x 496 5814 probe set(s) defined. > envsccdf <- as(sccdf, "environment") > raw@cdfName <- "sccdf" > boxplot(raw) Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : Invalid object for as.environment > raw@cdfName [1] "sccdf" > getCdfEnvAffy(raw) Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : Invalid object for as.environment > class(sccdf) [1] "CdfEnvAffy" attr(,"package") [1] "altcdfenvs" > raw@cdfName <- "envsccdf" > class(envsccdf) [1] "environment" > boxplot(raw) Error in ans[[i]][, i.probes] : incorrect number of dimensions Any help will be highly appreicated. Xiwei Wu, MD, PhD Assistant Research Scientist Department of Biomedical Informatics Beckman Research Insitute City of Hope National Medical Center Duarte, CA 91010 Phone: (626) 359-8111 ext. 65071 "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- -------- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}