cheers Martin, that makes sense. as much as i love a bit of recursion, I'll submit a patch to Pan Du & hopefully he can update lumi. cheers, Mark On 11/10/2012, at 3:33 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 10/10/2012 09:25 PM, Mark Cowley wrote: >> Thanks Martin, >> Unfortunately, explicitly specifying lumi::combine seems to interfere with the S4 calling mechanism in an interactive session: >> >> ### only lumi >> library(lumi) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method > > I can replicate that with example(LumiBatch) and then > > lumi::combine(example.lumi[,1], example.lumi[,2], example.lumi[,3]) > > I'd say this was an issue in methods, and the work-around (again!) would be to make the recursion here > > > lumi::combine > nonstandardGenericFunction for "combine" defined from package "BiocGenerics" > > function (x, y, ...) > { > if (length(list(...)) > 0L) { > callGeneric(x, do.call(callGeneric, list(y, ...))) > } > else { > standardGeneric("combine") > } > } > <environment: 0x1f53748=""> > > into an iteration: > > res = example.lumi[,1] > for (i in 2:3) > res = combine(res, example.lumi[,i]) > > Martin > >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "LumiBatch" >> >> ##### gdata then lumi >> library(gdata) >> library(lumi) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "LumiBatch" >> >> #### lumi then gdata >> library(lumi) >> library(gdata) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "data.frame" >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> [7] base >> >> other attached packages: >> [1] gdata_2.11.0 lumi_2.8.0 nleqslv_1.9.3 >> [4] methylumi_2.2.0 ggplot2_0.9.1 reshape2_1.2.1 >> [7] scales_0.2.1 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.34.0 affyio_1.24.0 >> [3] annotate_1.34.1 AnnotationDbi_1.18.1 >> [5] bigmemory_4.2.11 BiocInstaller_1.4.7 >> [7] Biostrings_2.24.1 bitops_1.0-4.1 >> [9] BSgenome_1.24.0 colorspace_1.1-1 >> [11] DBI_0.2-5 dichromat_1.2-4 >> [13] digest_0.5.2 DNAcopy_1.30.0 >> [15] GenomicRanges_1.8.12 genoset_1.6.0 >> [17] grid_2.15.1 gtools_2.7.0 >> [19] hdrcde_2.16 IRanges_1.14.4 >> [21] KernSmooth_2.23-8 labeling_0.1 >> [23] lattice_0.20-10 MASS_7.3-20 >> [25] Matrix_1.0-6 memoise_0.1 >> [27] mgcv_1.7-20 munsell_0.3 >> [29] nlme_3.1-104 plyr_1.7.1 >> [31] preprocessCore_1.18.0 proto_0.3-9.2 >> [33] RColorBrewer_1.0-5 RCurl_1.91-1 >> [35] Rsamtools_1.8.6 RSQLite_0.11.1 >> [37] rtracklayer_1.16.3 stats4_2.15.1 >> [39] stringr_0.6.1 tools_2.15.1 >> [41] XML_3.9-4 xtable_1.7-0 >> [43] zlibbioc_1.2.0 >> >> >> Reordering my package loads so that lumi is last, and just using 'combine' works. >> >> cheers, >> Mark >> >> On 10/10/2012, at 7:06 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> >>> On 10/08/2012 09:40 PM, Mark Cowley wrote: >>>> Dear list, >>>> i'm trying to combine two LumiBatch objects, using the S4 combine("LumiBatch","LumiBatch") method, defined originally in BiocGenerics, and enhanced within lumi. >>>> In a fresh session, with just lumi loaded, everything works fine, i.e. I get a LumiBatch object. >>>> As soon as I load gdata, this breaks the combine method, instead returning a data.frame with very odd dimensions. This is true if I load gdata before, or after lumi. Note that showMethods("lumi") doesn't change after loading gdata. Any ideas? >>> >>> Hi Mark -- unfortunately, this is not easily avoidable. gdata (a CRAN package) defines its own function combine that masks the version used by lumi and other Bioconductor packages. The work-around is to invoke lumi's combine with, e.g., >>> >>> lumi::combine(x = example.lumi[, 1], y = example.lumi[, 3]) >>> >>> If gdata were in Bioconductor, we could coerce the author into writing a method for combine, as defined in BiocGenerics. If you were writing a package, then you could importMethodsFrom(lumi, combine) and use combine safely in your own package code whether or not gdata was on the search path. >>> >>> Martin >>> >>>> cheers, >>>> Mark >>>> >>>> ### lumi, then gdata >>>>> suppressPackageStartupMessages(library(lumi)) >>>> Warning messages: >>>> 1: found methods to import for function ?eapply? but not the generic itself >>>> 2: replacing previous import ?image? when loading ?graphics? >>>>> load("Rmisc/n525.RDa") >>>>> load("Rmisc/s295.RDa") >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "LumiBatch" >>>> attr(,"package") >>>> [1] "lumi" >>>> ## the expected output >>>> >>>>> suppressPackageStartupMessages(library(gdata)) >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="environment", y="environment" >>>> (inherited from: x="AssayData", y="AssayData") >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "data.frame" >>>>> >>>> >>>> >>>> #### gdata then lumi >>>>> suppressPackageStartupMessages(library(gdata)) >>>>> suppressPackageStartupMessages(library(lumi)) >>>> Warning messages: >>>> 1: found methods to import for function ?eapply? but not the generic itself >>>> 2: replacing previous import ?image? when loading ?graphics? >>>>> load("Rmisc/n525.RDa") >>>>> load("Rmisc/s295.RDa") >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "LumiBatch" >>>> attr(,"package") >>>> [1] "lumi" >>>> >>>> >>>>> sessionInfo() >>>> R version 2.15.1 (2012-06-22) >>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>> >>>> locale: >>>> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] lumi_2.10.0 nleqslv_1.9.4 Biobase_2.18.0 BiocGenerics_0.4.0 >>>> [5] gdata_2.12.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affy_1.36.0 affyio_1.26.0 annotate_1.36.0 >>>> [4] AnnotationDbi_1.20.0 BiocInstaller_1.8.1 colorspace_1.1-1 >>>> [7] DBI_0.2-5 grid_2.15.1 gtools_2.7.0 >>>> [10] IRanges_1.16.2 KernSmooth_2.23-8 lattice_0.20-10 >>>> [13] MASS_7.3-22 Matrix_1.0-9 methylumi_2.4.0 >>>> [16] mgcv_1.7-21 nlme_3.1-104 parallel_2.15.1 >>>> [19] preprocessCore_1.20.0 RSQLite_0.11.2 stats4_2.15.1 >>>> [22] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >>> -- >>> 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 >> > > > -- > 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

Hi again, Your workaround definitely works in an interactive session, but I was expecting to fix the problem by fixing it within lumi::combine? I rebuilt & installed lumi after removing the recursion within lumi's combine, however even when explicitly calling lumi::combine I still got the error. it turns out that its the recursion that's still present within the BiocGenerics::combine function that throws the error, despite the signature(c("LumiBatch", "LumiBatch")) not being defined there? I've clearly got plenty of learning still to do with S4... cheers, Mark I changed code from: setMethod("combine", signature=c(x="LumiBatch", y="LumiBatch"), function(x, y, ...) { if (missing(y)) return(x) if (length(list(...)) > 0L) { callGeneric(x, do.call(callGeneric, list(y, ...))) ? to: setMethod("combine", signature=c(x="LumiBatch", y="LumiBatch"), function(x, y, ...) { if (missing(y)) return(x) if (length(list(...)) > 0) { res <- combine(x, y) extras <- list(...) for(i in seq(along=extras)) { res <- combine(res, extras[[i]]) } return( res ) } # ?. build, install, > library(lumi) > data(example.lumi) > lumi::combine(example.lumi[,1], example.lumi[,2], example.lumi[,3]) Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : 'callGeneric' must be called from a generic function or method > traceback() 3: stop("'callGeneric' must be called from a generic function or method") 2: callGeneric(x, do.call(callGeneric, list(y, ...))) 1: lumi::combine(example.lumi[, 1], example.lumi[, 2], example.lumi[, 3]) > lumi::combine nonstandardGenericFunction for "combine" defined from package "BiocGenerics" function (x, y, ...) { if (length(list(...)) > 0L) { callGeneric(x, do.call(callGeneric, list(y, ...))) } else { standardGeneric("combine") } } <environment: 0xc69b2c=""> ### ie, the one that's defined in BiocGenerics On 11/10/2012, at 3:33 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 10/10/2012 09:25 PM, Mark Cowley wrote: >> Thanks Martin, >> Unfortunately, explicitly specifying lumi::combine seems to interfere with the S4 calling mechanism in an interactive session: >> >> ### only lumi >> library(lumi) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method > > I can replicate that with example(LumiBatch) and then > > lumi::combine(example.lumi[,1], example.lumi[,2], example.lumi[,3]) > > I'd say this was an issue in methods, and the work-around (again!) would be to make the recursion here > > > lumi::combine > nonstandardGenericFunction for "combine" defined from package "BiocGenerics" > > function (x, y, ...) > { > if (length(list(...)) > 0L) { > callGeneric(x, do.call(callGeneric, list(y, ...))) > } > else { > standardGeneric("combine") > } > } > <environment: 0x1f53748=""> > > into an iteration: > > res = example.lumi[,1] > for (i in 2:3) > res = combine(res, example.lumi[,i]) > > Martin > >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "LumiBatch" >> >> ##### gdata then lumi >> library(gdata) >> library(lumi) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "LumiBatch" >> >> #### lumi then gdata >> library(lumi) >> library(gdata) >> load("Rmisc/n525.RDa") >> load("Rmisc/s217.RDa") >> load("Rmisc/s295.RDa") >> a <- lumi::combine(s217, n525, s295) >> Error in callGeneric(x, do.call(callGeneric, list(y, ...))) : >> 'callGeneric' must be called from a generic function or method >> >> a <- combine(s217, n525, s295) >> class(a) >> # [1] "data.frame" >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> [7] base >> >> other attached packages: >> [1] gdata_2.11.0 lumi_2.8.0 nleqslv_1.9.3 >> [4] methylumi_2.2.0 ggplot2_0.9.1 reshape2_1.2.1 >> [7] scales_0.2.1 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.34.0 affyio_1.24.0 >> [3] annotate_1.34.1 AnnotationDbi_1.18.1 >> [5] bigmemory_4.2.11 BiocInstaller_1.4.7 >> [7] Biostrings_2.24.1 bitops_1.0-4.1 >> [9] BSgenome_1.24.0 colorspace_1.1-1 >> [11] DBI_0.2-5 dichromat_1.2-4 >> [13] digest_0.5.2 DNAcopy_1.30.0 >> [15] GenomicRanges_1.8.12 genoset_1.6.0 >> [17] grid_2.15.1 gtools_2.7.0 >> [19] hdrcde_2.16 IRanges_1.14.4 >> [21] KernSmooth_2.23-8 labeling_0.1 >> [23] lattice_0.20-10 MASS_7.3-20 >> [25] Matrix_1.0-6 memoise_0.1 >> [27] mgcv_1.7-20 munsell_0.3 >> [29] nlme_3.1-104 plyr_1.7.1 >> [31] preprocessCore_1.18.0 proto_0.3-9.2 >> [33] RColorBrewer_1.0-5 RCurl_1.91-1 >> [35] Rsamtools_1.8.6 RSQLite_0.11.1 >> [37] rtracklayer_1.16.3 stats4_2.15.1 >> [39] stringr_0.6.1 tools_2.15.1 >> [41] XML_3.9-4 xtable_1.7-0 >> [43] zlibbioc_1.2.0 >> >> >> Reordering my package loads so that lumi is last, and just using 'combine' works. >> >> cheers, >> Mark >> >> On 10/10/2012, at 7:06 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> >>> On 10/08/2012 09:40 PM, Mark Cowley wrote: >>>> Dear list, >>>> i'm trying to combine two LumiBatch objects, using the S4 combine("LumiBatch","LumiBatch") method, defined originally in BiocGenerics, and enhanced within lumi. >>>> In a fresh session, with just lumi loaded, everything works fine, i.e. I get a LumiBatch object. >>>> As soon as I load gdata, this breaks the combine method, instead returning a data.frame with very odd dimensions. This is true if I load gdata before, or after lumi. Note that showMethods("lumi") doesn't change after loading gdata. Any ideas? >>> >>> Hi Mark -- unfortunately, this is not easily avoidable. gdata (a CRAN package) defines its own function combine that masks the version used by lumi and other Bioconductor packages. The work-around is to invoke lumi's combine with, e.g., >>> >>> lumi::combine(x = example.lumi[, 1], y = example.lumi[, 3]) >>> >>> If gdata were in Bioconductor, we could coerce the author into writing a method for combine, as defined in BiocGenerics. If you were writing a package, then you could importMethodsFrom(lumi, combine) and use combine safely in your own package code whether or not gdata was on the search path. >>> >>> Martin >>> >>>> cheers, >>>> Mark >>>> >>>> ### lumi, then gdata >>>>> suppressPackageStartupMessages(library(lumi)) >>>> Warning messages: >>>> 1: found methods to import for function ?eapply? but not the generic itself >>>> 2: replacing previous import ?image? when loading ?graphics? >>>>> load("Rmisc/n525.RDa") >>>>> load("Rmisc/s295.RDa") >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "LumiBatch" >>>> attr(,"package") >>>> [1] "lumi" >>>> ## the expected output >>>> >>>>> suppressPackageStartupMessages(library(gdata)) >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="environment", y="environment" >>>> (inherited from: x="AssayData", y="AssayData") >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "data.frame" >>>>> >>>> >>>> >>>> #### gdata then lumi >>>>> suppressPackageStartupMessages(library(gdata)) >>>>> suppressPackageStartupMessages(library(lumi)) >>>> Warning messages: >>>> 1: found methods to import for function ?eapply? but not the generic itself >>>> 2: replacing previous import ?image? when loading ?graphics? >>>>> load("Rmisc/n525.RDa") >>>>> load("Rmisc/s295.RDa") >>>>> showMethods("combine") >>>> Function: combine (package BiocGenerics) >>>> x="AnnotatedDataFrame", y="AnnotatedDataFrame" >>>> x="ANY", y="missing" >>>> x="AssayData", y="AssayData" >>>> x="data.frame", y="data.frame" >>>> x="eSet", y="eSet" >>>> x="ExpressionSet", y="LumiBatch" >>>> x="LumiBatch", y="ExpressionSet" >>>> x="LumiBatch", y="LumiBatch" >>>> x="matrix", y="matrix" >>>> x="MethyLumiM", y="MethyLumiM" >>>> x="MethyLumiQC", y="MethyLumiQC" >>>> x="MethyLumiSet", y="MethyLumiSet" >>>> x="MIAME", y="MIAME" >>>> >>>>> a <- combine(n525, s295) >>>>> class(a) >>>> [1] "LumiBatch" >>>> attr(,"package") >>>> [1] "lumi" >>>> >>>> >>>>> sessionInfo() >>>> R version 2.15.1 (2012-06-22) >>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>> >>>> locale: >>>> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] lumi_2.10.0 nleqslv_1.9.4 Biobase_2.18.0 BiocGenerics_0.4.0 >>>> [5] gdata_2.12.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affy_1.36.0 affyio_1.26.0 annotate_1.36.0 >>>> [4] AnnotationDbi_1.20.0 BiocInstaller_1.8.1 colorspace_1.1-1 >>>> [7] DBI_0.2-5 grid_2.15.1 gtools_2.7.0 >>>> [10] IRanges_1.16.2 KernSmooth_2.23-8 lattice_0.20-10 >>>> [13] MASS_7.3-22 Matrix_1.0-9 methylumi_2.4.0 >>>> [16] mgcv_1.7-21 nlme_3.1-104 parallel_2.15.1 >>>> [19] preprocessCore_1.20.0 RSQLite_0.11.2 stats4_2.15.1 >>>> [22] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >>> -- >>> 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 >> > > > -- > 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