[BioC] lumi - Heatmap

[Paolo Kunderfranco]

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