Dear All, I would like to create a heatmap of a subset of probe_ID extracted from a expression dataMatrix processed with lumi package. > head(DataMatrix) A B C D WpaZ9x9f_hAnoR.VBE 11.508089 10.294538 12.389376 11.808273 ZhdXp75JftSF3iWLF4 9.209168 8.577338 10.420710 9.609604 xnx7ijE2CcOSlY55eA 9.025774 8.427950 9.766751 9.599868 xPkUXaq37oR_vSi6HY 10.773646 9.615071 11.371380 11.125862 BRRdqrfuhH69KLodsc 10.295491 9.351849 10.986417 10.784596 upNer6bJTpt27XeZe4 11.671597 10.937059 13.688076 12.747410 > head(probe_ID) [1] "WpaZ9x9f_hAnoR.VBE" "xPkUXaq37oR_vSi6HY" "BRRdqrfuhH69KLodsc" "ZqRKnn0K14kTIep1.c" "EqQqefQrXiRMh6nX9w" "6nhvEuw4uB13jt.gH8" I tried like this but it seems not working: >DataMatrix[DataMatrix[,0] %in% probe_ID, DataMatrix] how do I proceed? any help? moreover is there a way to plot Target_ID instead of Probe_ID in the final heatmap? heatmap(DataMatrix[1:10,]) Thanks, Paolo > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C [5] LC_TIME=Italian_Italy.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.34.1 lumiMouseAll.db_1.18.0 org.Mm.eg.db_2.7.1 limma_3.12.1 lumiMouseIDMapping_1.10.0 [6] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.1 lumi_2.8.0 nleqslv_1.9.3 [11] methylumi_2.2.0 ggplot2_0.9.1 reshape2_1.2.1 scales_0.2.1 Biobase_2.16.0 [16] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 bigmemory_4.2.11 BiocInstaller_1.4.7 Biostrings_2.24.1 bitops_1.0-4.1 [7] BSgenome_1.24.0 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 DNAcopy_1.30.0 GenomicRanges_1.8.10 [13] genoset_1.6.0 grid_2.15.0 hdrcde_2.16 IRanges_1.14.4 KernSmooth_2.23-8 labeling_0.1 [19] lattice_0.20-6 MASS_7.3-19 Matrix_1.0-7 memoise_0.1 mgcv_1.7-19 munsell_0.3 [25] nlme_3.1-104 plyr_1.7.1 preprocessCore_1.18.0 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1.1 [31] Rsamtools_1.8.5 rtracklayer_1.16.3 stats4_2.15.0 stringr_0.6.1 tools_2.15.0 XML_3.9-4.1 [37] xtable_1.7-0 zlibbioc_1.2.0

On Mon, Aug 27, 2012 at 6:54 AM, Paolo Kunderfranco < paolo.kunderfranco@gmail.com> wrote: > Dear All, > > I would like to create a heatmap of a subset of probe_ID extracted > from a expression dataMatrix processed with lumi package. > > > head(DataMatrix) > A B C > D > WpaZ9x9f_hAnoR.VBE 11.508089 10.294538 12.389376 11.808273 > ZhdXp75JftSF3iWLF4 9.209168 8.577338 10.420710 9.609604 > xnx7ijE2CcOSlY55eA 9.025774 8.427950 9.766751 9.599868 > xPkUXaq37oR_vSi6HY 10.773646 9.615071 11.371380 11.125862 > BRRdqrfuhH69KLodsc 10.295491 9.351849 10.986417 10.784596 > upNer6bJTpt27XeZe4 11.671597 10.937059 13.688076 12.747410 > > > head(probe_ID) > [1] "WpaZ9x9f_hAnoR.VBE" "xPkUXaq37oR_vSi6HY" "BRRdqrfuhH69KLodsc" > "ZqRKnn0K14kTIep1.c" "EqQqefQrXiRMh6nX9w" "6nhvEuw4uB13jt.gH8" > > I tried like this but it seems not working: > > >DataMatrix[DataMatrix[,0] %in% probe_ID, DataMatrix] > > Hi, Paolo. Probably something like this will work assuming that the probe IDs are actually row names. heatmap(DataMatrix[probe_ID,]) > moreover is there a way to plot Target_ID instead of Probe_ID in the > final heatmap? > See the help for heatmap and the labRow and labCol arguments. Sean > > heatmap(DataMatrix[1:10,]) > > Thanks, > Paolo > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 > LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C > [5] LC_TIME=Italian_Italy.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annotate_1.34.1 lumiMouseAll.db_1.18.0 > org.Mm.eg.db_2.7.1 limma_3.12.1 > lumiMouseIDMapping_1.10.0 > [6] RSQLite_0.11.1 DBI_0.2-5 > AnnotationDbi_1.18.1 lumi_2.8.0 nleqslv_1.9.3 > [11] methylumi_2.2.0 ggplot2_0.9.1 > reshape2_1.2.1 scales_0.2.1 Biobase_2.16.0 > [16] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affy_1.34.0 affyio_1.24.0 bigmemory_4.2.11 > BiocInstaller_1.4.7 Biostrings_2.24.1 bitops_1.0-4.1 > [7] BSgenome_1.24.0 colorspace_1.1-1 dichromat_1.2-4 > digest_0.5.2 DNAcopy_1.30.0 GenomicRanges_1.8.10 > [13] genoset_1.6.0 grid_2.15.0 hdrcde_2.16 > IRanges_1.14.4 KernSmooth_2.23-8 labeling_0.1 > [19] lattice_0.20-6 MASS_7.3-19 Matrix_1.0-7 > memoise_0.1 mgcv_1.7-19 munsell_0.3 > [25] nlme_3.1-104 plyr_1.7.1 preprocessCore_1.18.0 > proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1.1 > [31] Rsamtools_1.8.5 rtracklayer_1.16.3 stats4_2.15.0 > stringr_0.6.1 tools_2.15.0 XML_3.9-4.1 > [37] xtable_1.7-0 zlibbioc_1.2.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]