[BioC] cummerbund how to get matrix for csheatmap

Adrian Johnson oriolebaltimore at gmail.com
Fri Mar 1 19:05:42 CET 2013

I am trying to plot the most significant genes. I have 3 different
sample types and 4 replicates each. Could anyone suggest how do I get
the matrix of fpkm values that was plotted in csHeatmap function.

> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.001)
> diffGenes<-getGenes(cuff,diffGeneIDs)

the heatmap gene names are not visible. I want to get the matrix for h
and plot heatmap using another heatmap function.
How do I get the matrix for h.


> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] cummeRbund_2.0.0     Gviz_1.2.1           rtracklayer_1.18.2
GenomicRanges_1.10.7 IRanges_1.16.6       fastcluster_1.1.8
 [8] ggplot2_0.9.3        RSQLite_0.11.2       DBI_0.2-5

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.4   Biobase_2.18.0         biomaRt_2.14.0
   Biostrings_2.26.3      biovizBase_1.6.2       bitops_1.0-5
 [7] BSgenome_1.26.1        cluster_1.14.3         colorspace_1.2-1
   dichromat_2.0-0        digest_0.6.3
[13] gtable_0.1.2           Hmisc_3.10-1           labeling_0.1
   lattice_0.20-13        MASS_7.3-23            munsell_0.4
[19] parallel_2.15.2        plyr_1.8               proto_0.3-10
   RColorBrewer_1.0-5     RCurl_1.95-3           Rsamtools_1.10.2
[25] scales_0.2.3           stats4_2.15.2          stringr_0.6.2
   tools_2.15.2           XML_3.95-0.1           zlibbioc_1.4.0

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