Dear list, I've just come across this somewhat unexpected clash between the oligo and gdata packages. gdata is required for gplots, and is therefore loaded whenever I plan on using heatmaps - basically always for microarray data. However, once gdata in loaded the read.celfiles() functions fails. Probably due to some issues with combine? As such this can easily be avoided; just thought I'd report it here in case anyone comes across the same when using oligo. See example and sessionInfo below. Thanks \Heidi > library(Biobase) Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(oligo) Loading required package: oligoClasses Loading required package: preprocessCore Welcome to oligo version 1.10.0 > library(pd.mogene.1.0.st.v1) Loading required package: RSQLite Loading required package: DBI Warning message: package 'pd.mogene.1.0.st.v1' was built under R version 2.10.1 > files<- list.celfiles("Data", full.name=TRUE) > raw<- read.celfiles(files[1:3]) Platform design info loaded. Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz Warning message: In AffyDate2Posix(datetime) : Returning dates/times as strings - format not recognized. > library(gplots) Loading required package: gtools Loading required package: gdata Attaching package: 'gdata' The following object(s) are masked from package:Biobase : combine The following object(s) are masked from package:utils : object.size Loading required package: caTools Loading required package: bitops Loading required package: grid Attaching package: 'gplots' The following object(s) are masked from package:stats : lowess > raw<- read.celfiles(files[1:3]) Platform design info loaded. Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class structure("AnnotatedDataFrame", package = "Biobase") into a data.frame In addition: Warning message: In AffyDate2Posix(datetime) : Returning dates/times as strings - format not recognized. > detach("package:gdata") > raw<- read.celfiles(files[1:3]) Platform design info loaded. Reading in : Data/A1-1_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-2_(HuGene-1_0-st-v1)_2.CEL.gz Reading in : Data/A1-3_(HuGene-1_0-st-v1)_2.CEL.gz Warning message: In AffyDate2Posix(datetime) : Returning dates/times as strings - format not recognized. > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin8.11.1 locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] gplots_2.7.3 caTools_1.10 [3] bitops_1.0-4.1 gtools_2.6.1 [5] pd.mogene.1.0.st.v1_3.0.0 RSQLite_0.7-3 [7] DBI_0.2-4 oligo_1.10.0 [9] preprocessCore_1.8.0 oligoClasses_1.8.0 [11] Biobase_2.6.0 loaded via a namespace (and not attached): [1] Biostrings_2.14.1 IRanges_1.4.1 affxparser_1.18.0 affyio_1.14.0 [5] gdata_2.6.1 splines_2.10.0 >