D'oh. Not sure what's going on here. Google leads me to this: https://code.google.com/p/renjin/ Which is very cool, but does not solve my present problem. I can't seem to pull a matrix out of an eSet-derived object, which is making life difficult at the moment. R> sessionInfo() R Under development (unstable) (2012-10-08 r60907) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] MASS_7.3-22 methylumi_2.5.0 ggplot2_0.9.2.1 reshape2_1.2.1 [5] scales_0.2.2 impute_1.33.0 regulatoR_0.9.25 FDb.InfiniumMethylation.hg19_1.0.4 [9] Biostrings_2.27.2 GenomicFeatures_1.11.1 AnnotationDbi_1.21.0 rtracklayer_1.19.0 [13] GenomicRanges_1.11.0 IRanges_1.17.0 Matrix_1.0-9 lattice_0.20-10 [17] Biobase_2.19.0 BiocGenerics_0.5.0 BiocInstaller_1.9.4 dataframe_2.5 [21] devtools_0.8 gtools_2.7.0 loaded via a namespace (and not attached): [1] annotate_1.37.0 biomaRt_2.15.0 bitops_1.0-4.1 BSgenome_1.27.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 edgeR_3.1.0 [10] evaluate_0.4.2 grid_2.16.0 gtable_0.1.1 httr_0.1.1 labeling_0.1 limma_3.15.2 memoise_0.1 munsell_0.4 parallel_2.16.0 [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.95-0.1.2 Repitools_1.5.0 Rsamtools_1.11.1 RSQLite_0.11.2 stats4_2.16.0 stringr_0.6.1 [28] tools_2.16.0 whisker_0.1 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.5.0 -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

An example would be great. But I am guessing this is related to R-core making it much harder to access the C core. Essentially, R_shortRowNames is now unexported (guessing). Kasper On Wed, Oct 10, 2012 at 3:04 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > D'oh. Not sure what's going on here. Google leads me to this: > > https://code.google.com/p/renjin/ > > Which is very cool, but does not solve my present problem. I can't seem to > pull a matrix out of an eSet-derived object, which is making life difficult > at the moment. > > R> sessionInfo() > R Under development (unstable) (2012-10-08 r60907) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] MASS_7.3-22 methylumi_2.5.0 > ggplot2_0.9.2.1 reshape2_1.2.1 > [5] scales_0.2.2 impute_1.33.0 > regulatoR_0.9.25 FDb.InfiniumMethylation.hg19_1.0.4 > [9] Biostrings_2.27.2 GenomicFeatures_1.11.1 > AnnotationDbi_1.21.0 rtracklayer_1.19.0 > [13] GenomicRanges_1.11.0 IRanges_1.17.0 > Matrix_1.0-9 lattice_0.20-10 > [17] Biobase_2.19.0 BiocGenerics_0.5.0 > BiocInstaller_1.9.4 dataframe_2.5 > [21] devtools_0.8 gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] annotate_1.37.0 biomaRt_2.15.0 bitops_1.0-4.1 > BSgenome_1.27.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > digest_0.5.2 edgeR_3.1.0 > [10] evaluate_0.4.2 grid_2.16.0 gtable_0.1.1 httr_0.1.1 > labeling_0.1 limma_3.15.2 memoise_0.1 munsell_0.4 > parallel_2.16.0 > [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > RCurl_1.95-0.1.2 Repitools_1.5.0 Rsamtools_1.11.1 RSQLite_0.11.2 > stats4_2.16.0 stringr_0.6.1 > [28] tools_2.16.0 whisker_0.1 XML_3.95-0.1 xtable_1.7-0 > zlibbioc_1.5.0 > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Hi Tim, You can use .Internal(shortRowNames(x, type)) or base:::.row_names_info(x, type) instead. But keep in mind that, like .Call("R_shortRowNames", x, type, PACKAGE="base") those things are not part of the API so they will break too the day R core decides to change them to something else. AFAICT, this is low-level stuff for accessing the internals of a data frame. After a quick look at the code, it seems that only 0L, 1L, or 2L are valid 'type' values: > x <- data.frame(aa=letters[1:6]) > x aa 1 a 2 b 3 c 4 d 5 e 6 f > y <- data.frame(aa=letters[1:6], row.names=1:6) > y aa 1 a 2 b 3 c 4 d 5 e 6 f > identical(x, y) [1] TRUE > identical(x, y, attrib.as.set=FALSE) [1] FALSE > base:::.row_names_info(x, type=2L) [1] 6 > base:::.row_names_info(y, type=2L) [1] 6 > base:::.row_names_info(x, type=1L) [1] -6 > base:::.row_names_info(y, type=1L) [1] 6 > base:::.row_names_info(x, type=0L) [1] NA -6 > base:::.row_names_info(y, type=0L) [1] NA 6 I wonder what are the reasons for using this in a package instead of higher-level nrow(x) and rownames(x), which are part of the API and documented. H. On 10/10/2012 12:04 PM, Tim Triche, Jr. wrote: > D'oh. Not sure what's going on here. Google leads me to this: > > https://code.google.com/p/renjin/ > > Which is very cool, but does not solve my present problem. I can't seem to > pull a matrix out of an eSet-derived object, which is making life difficult > at the moment. > > R> sessionInfo() > R Under development (unstable) (2012-10-08 r60907) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] MASS_7.3-22 methylumi_2.5.0 > ggplot2_0.9.2.1 reshape2_1.2.1 > [5] scales_0.2.2 impute_1.33.0 > regulatoR_0.9.25 FDb.InfiniumMethylation.hg19_1.0.4 > [9] Biostrings_2.27.2 GenomicFeatures_1.11.1 > AnnotationDbi_1.21.0 rtracklayer_1.19.0 > [13] GenomicRanges_1.11.0 IRanges_1.17.0 > Matrix_1.0-9 lattice_0.20-10 > [17] Biobase_2.19.0 BiocGenerics_0.5.0 > BiocInstaller_1.9.4 dataframe_2.5 > [21] devtools_0.8 gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] annotate_1.37.0 biomaRt_2.15.0 bitops_1.0-4.1 > BSgenome_1.27.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 > digest_0.5.2 edgeR_3.1.0 > [10] evaluate_0.4.2 grid_2.16.0 gtable_0.1.1 httr_0.1.1 > labeling_0.1 limma_3.15.2 memoise_0.1 munsell_0.4 > parallel_2.16.0 > [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > RCurl_1.95-0.1.2 Repitools_1.5.0 Rsamtools_1.11.1 RSQLite_0.11.2 > stats4_2.16.0 stringr_0.6.1 > [28] tools_2.16.0 whisker_0.1 XML_3.95-0.1 xtable_1.7-0 > zlibbioc_1.5.0 > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319