Hi all, I went through the excellent tutorial at http://www.bioconductor.org/repository/devel/vignette/ngenomeschips.pd f regarding how to make an alternative CDF environment for affy chips. I'm using HG-U133a2 chips. This is R 2.0.1 on OSX 10.3 with all BC libraries updated.. Briefly, I did this -- 1)made a cdf with a subset of 1,571 probes (out of 22277) that i wanted to keep for re-analysis by following the tutorial. 2) saved the cdf save(m5_CDF, file = "m5_CDF.Rdata") 3) loaded the CDF into a blank workspace. load(file = "m5_CDF.Rdata") ls() [1] "m5_CDF" str(m5_CDF) Loading required package: altcdfenvs Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: affy Loading required package: reposTools Loading required package: matchprobes Loading required package: hgu95acdf Loading required package: hgu133aprobe Loading required package: plasmodiumanophelescdf Attaching package 'plasmodiumanophelescdf': The following object(s) are masked from package:hgu95acdf : i2xy xy2i Formal class 'CdfEnvAffy' [package "altcdfenvs"] with 8 slots ..@ envir :length 1571 <environment> ..@ envName : chr "m5_filtered_probesets_only" ..@ index2xy :function (object, i) ..@ xy2index :function (object, x, y) ..@ nrow : int 732 ..@ ncol : int 732 ..@ probeTypes: chr [1:2] "pm" "mm" ..@ chipType : chr "hgu133a2cdf" 4) put 6 HG-U133a2 .CEL files into the working dir. and read cel files into workspace. m5 <- ReadAffy() str(m5) Formal class 'AffyBatch' [package "affy"] with 9 slots ..@ cdfName : chr "HG-U133A_2" ..@ nrow : int 732 ..@ ncol : int 732 ..@ exprs : num [1:535824, 1:6] 128 6360 110 6760 112 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:6] "199.CEL" "200.CEL" "201.CEL" "202.CEL" ... ..@ se.exprs : logi[0 , 0 ] ..@ phenoData :Formal class 'phenoData' [package "Biobase"] with 2 slots .. .. ..@ pData.sample : int [1:6] 1 2 3 4 5 6 .. .. ..@ varLabels.sample: chr "arbitrary numbering" ..@ description:Formal class 'MIAME' [package "Biobase"] with 11 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations: list() .. .. ..@ normControls : list() .. .. ..@ preprocessing :List of 2 .. .. .. ..$ filenames :List of 6 .. .. .. .. ..$ : chr "/199.CEL" .. .. .. .. ..$ : chr "/200.CEL" .. .. .. .. ..$ : chr "/201.CEL" .. .. .. .. ..$ : chr "/202.CEL" .. .. .. .. ..$ : chr "/203.CEL" .. .. .. .. ..$ : chr "/204.CEL" .. .. .. ..$ affyversion: chr NA .. .. ..@ other : list() ..@ annotation : chr "hgu133a2" ..@ notes : chr "" 5) set cdfName slot of m5 affybatch object to my CDF name.. m5@cdfName <- "m5_CDF" 6) tried rma. m5rma <- rma(m5) Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : Invalid object for as.environment 7) tried gcrma library(gcrma) m5gcrma <- gcrma(m5) Computing affinities[1] "Checking to see if your internet connection works..." Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Error in getCDF(cdfpackagename) : Environment m5cdfcdf was not found in the Bioconductor repository. I'm not sure how to either set the environment for rma, or set cdfpackagename for gcrma...? The aforementioned tutorial was great for how to create the CDF, but after that I can't seem to find out any more information on what to do next as far as normalization goes... Thanks for any help, Ken