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Adrian Johnson
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330
@adrian-johnson-2728
Last seen 4.6 years ago
Hi:
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)
>h<-csHeatmap(diffGenes,cluster='both')
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.
thanks
Adrian
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[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
States.1252
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
reshape2_1.2.2
[8] ggplot2_0.9.3 RSQLite_0.11.2 DBI_0.2-5
BiocGenerics_0.4.0
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
GenomicFeatures_1.10.2
[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