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]]

