Dear I am investigating whether affyPara can be used to analyze a large number of Microarray data. As a test case I have 20 CEL files. This works just fine running ... expressionSetRma<- rmaPara(files) ... If I want to use the "cdfname" parameter however ... expressionSetRma<- rmaPara(files, cdfname="hgu133plus2hsentrezg", verbose=TRUE) ... I receive following error: Error in dimnames(eset_mat) <- list(ids, samples.names) : length of 'dimnames' [1] not equal to array extent Calls: rmaPara -> preproPara -> .doSummarizationPara In addition: Warning messages: 1: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' Execution halted I saw a thread http://answerpot.com/showthread.php?1408276-affyPara mentioning a bug in the .initAffyBatchSF function date 21/10/2010. Might this be the same bug ? Many thanks for your help and/or ideas. Kind Regards Yves Wetzels Contractor on behalf of Janssen Turnhoutseweg 30 B-2340-Beerse, Belgium Below you`ll find the logfile/environment settings for both test runs. ****************************************************************** Log for expressionSetRma<- rmaPara(files) => OK ****************************************************************** ubuntu at ip-10-239-95-215:~/test$ cat runAffyPara.R.log.withoutcdf R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affyPara) Loading required package: affy Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: snow Loading required package: vsn Loading required package: aplpack Loading required package: tcltk Loading Tcl/Tk interface ... done Attaching package: ?affyPara? The following object(s) are masked from ?package:snow?: makeCluster, stopCluster Warning message: In fun(libname, pkgname) : no DISPLAY variable so Tk is not available > library(hgu133plus2hsentrezgcdf) > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133plus2hsentrezgcdf_12.1.0 affyPara_1.16.0 [3] aplpack_1.2.6 vsn_3.24.0 [5] snow_0.3-9 affy_1.34.0 [7] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.6 grid_2.15.0 [4] lattice_0.20-6 limma_3.12.1 preprocessCore_1.18.0 [7] tools_2.15.0 zlibbioc_1.2.0 > path <- "/home/ubuntu/test/cel_files" > makeCluster(2) > files <- list.celfiles(path, full.names=TRUE) > files [1] "/home/ubuntu/test/cel_files/GSM686287.CEL" [2] "/home/ubuntu/test/cel_files/GSM686289.CEL" [3] "/home/ubuntu/test/cel_files/GSM686290.CEL" [4] "/home/ubuntu/test/cel_files/GSM686291.CEL" [5] "/home/ubuntu/test/cel_files/GSM686298.CEL" [6] "/home/ubuntu/test/cel_files/GSM686300.CEL" [7] "/home/ubuntu/test/cel_files/GSM686301.CEL" [8] "/home/ubuntu/test/cel_files/GSM686303.CEL" [9] "/home/ubuntu/test/cel_files/GSM686304.CEL" [10] "/home/ubuntu/test/cel_files/GSM686305.CEL" [11] "/home/ubuntu/test/cel_files/GSM686310.CEL" [12] "/home/ubuntu/test/cel_files/GSM686311.CEL" [13] "/home/ubuntu/test/cel_files/GSM686314.CEL" [14] "/home/ubuntu/test/cel_files/GSM686316.CEL" [15] "/home/ubuntu/test/cel_files/GSM686319.CEL" [16] "/home/ubuntu/test/cel_files/GSM686320.CEL" [17] "/home/ubuntu/test/cel_files/GSM686322.CEL" [18] "/home/ubuntu/test/cel_files/GSM686323.CEL" [19] "/home/ubuntu/test/cel_files/GSM686324.CEL" [20] "/home/ubuntu/test/cel_files/GSM686325.CEL" > expressionSetRma<- rmaPara(files) Loading required package: AnnotationDbi Attaching package: ?hgu133plus2cdf? The following object(s) are masked from ?package:hgu133plus2hsentrezgcdf?: i2xy, xy2i Warning messages: 1: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' > stopCluster() > write.exprs(expressionSetRma,file="/home/ubuntu/test/expressionSetRm a.Rda") > ****************************************************************** Log for expressionSetRma<- rmaPara(files) => ERROR ****************************************************************** ubuntu at ip-10-239-95-215:~/test$ more runAffyPara.R.log.withcdf R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affyPara) Loading required package: affy Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: snow Loading required package: vsn Loading required package: aplpack Loading required package: tcltk Loading Tcl/Tk interface ... done Attaching package: ?affyPara? The following object(s) are masked from ?package:snow?: makeCluster, stopCluster Warning message: In fun(libname, pkgname) : no DISPLAY variable so Tk is not available > library(hgu133plus2hsentrezgcdf) > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133plus2hsentrezgcdf_12.1.0 affyPara_1.16.0 [3] aplpack_1.2.6 vsn_3.24.0 [5] snow_0.3-9 affy_1.34.0 [7] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.6 grid_2.15.0 [4] lattice_0.20-6 limma_3.12.1 preprocessCore_1.18.0 [7] tools_2.15.0 zlibbioc_1.2.0 > path <- "/home/ubuntu/test/cel_files" > makeCluster(2) > files <- list.celfiles(path, full.names=TRUE) > files [1] "/home/ubuntu/test/cel_files/GSM686287.CEL" [2] "/home/ubuntu/test/cel_files/GSM686289.CEL" [3] "/home/ubuntu/test/cel_files/GSM686290.CEL" [4] "/home/ubuntu/test/cel_files/GSM686291.CEL" [5] "/home/ubuntu/test/cel_files/GSM686298.CEL" [6] "/home/ubuntu/test/cel_files/GSM686300.CEL" [7] "/home/ubuntu/test/cel_files/GSM686301.CEL" [8] "/home/ubuntu/test/cel_files/GSM686303.CEL" [9] "/home/ubuntu/test/cel_files/GSM686304.CEL" [10] "/home/ubuntu/test/cel_files/GSM686305.CEL" [11] "/home/ubuntu/test/cel_files/GSM686310.CEL" [12] "/home/ubuntu/test/cel_files/GSM686311.CEL" [13] "/home/ubuntu/test/cel_files/GSM686314.CEL" [14] "/home/ubuntu/test/cel_files/GSM686316.CEL" [15] "/home/ubuntu/test/cel_files/GSM686319.CEL" [16] "/home/ubuntu/test/cel_files/GSM686320.CEL" [17] "/home/ubuntu/test/cel_files/GSM686322.CEL" [18] "/home/ubuntu/test/cel_files/GSM686323.CEL" [19] "/home/ubuntu/test/cel_files/GSM686324.CEL" [20] "/home/ubuntu/test/cel_files/GSM686325.CEL" > expressionSetRma<- rmaPara(files, cdfname="hgu133plus2hsentrezg", verbose=TRUE) Error in dimnames(eset_mat) <- list(ids, samples.names) : length of 'dimnames' [1] not equal to array extent Calls: rmaPara -> preproPara -> .doSummarizationPara In addition: Warning messages: 1: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4' Execution halted