That helps a lot Martin, thank you so much. Just for the record, the problem can be reproduced in the following manner: library(Biobase) set.seed(1) x = matrix(rnorm(100), nc=5) y = annotatedDataFrameFrom(x, TRUE) z1 = combine(y, y) library(gdata) z2 = combine(y, y) b On Tue, Feb 2, 2010 at 1:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 02/02/2010 03:58 AM, Benilton Carvalho wrote: >> Hi Heidi, >> >> Yes, the issue is with combine(). >> >> In Biobase, its generic function is defined as function(x, y, ...) >> >> In gdata, it is defined as function(...) >> >> As the warning says, gdata::combine masks Biobase::combine. >> >> Before I make any change, I'll wait until I hear from the gdata and >> Biobase maintainers. > > Hi Benilton, Heidi -- > > I saw the original post but it's not a reproducible example and there > wasn't any traceback() so I didn't chime in. I guess this is from one of > the three uses of combine() in oligo::getMetadata or oligo::getMetadata2 > and the solution is likely for oligo to importMethodsFrom(Biobase, > combine) in its NAMESPACE. If the issue is somehow more subtle (e.g., > oligo wanting to use both gdata and Biobase combine) then the solution > is to use Biobase::combine. A similar solution (import combine from > Biobase) is appropriate if the problem call is from a function defined > in a package different from oligo. > > If the problem is in Heidi's 'user' code then the solution is for Heidi > to use Biobase::combine. > > Hope that helps. > > Martin > >> >> b >> >> On Thu, Jan 28, 2010 at 10:57 PM, Heidi Dvinge <heidi at="" ebi.ac.uk=""> wrote: >>> 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 >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 >