Hi Justin,
GSVA does not work correctly with LumiBatch objects. It does all the
calculations, but then returns the original input data object, not the pathway
collapsed version of the input data.
library(lumi)
library(GSVA)
library(GSVAdata)
library(lumiHumanAll.db)
data(example.lumi)
data(c2BroadSets)
res.eset <- gsva(example.lumi, c2BroadSets)$es.obs
res.matrix <- gsva(exprs(example.lumi), c2BroadSets,
annotation=annotation(example.lumi))$es.obs
> dim(res.eset)
Features Samples
8000 4
> dim(res.matrix)
[1] 2986 4
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] lumiHumanAll.db_1.22.0 GSVAdata_0.99.11 hgu95a.db_2.10.1
[4] org.Hs.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7
[7] GSVA_1.10.1 GSEABase_1.24.0 graph_1.40.1
[10] annotate_1.40.0 AnnotationDbi_1.24.0 lumi_2.14.1
[13] Biobase_2.22.0 BiocGenerics_0.8.0 knitr_1.5
loaded via a namespace (and not attached):
[1] affy_1.40.0 affyio_1.30.0 base64_1.1
[4] beanplot_1.1 BiocInstaller_1.12.0 biomaRt_2.18.0
[7] Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.30.0
[10] bumphunter_1.2.0 codetools_0.2-8 colorspace_1.2-4
[13] digest_0.6.4 doRNG_1.5.5 evaluate_0.5.1
[16] foreach_1.4.1 formatR_0.10 genefilter_1.44.0
[19] GenomicFeatures_1.14.2 GenomicRanges_1.14.4 grid_3.0.2
[22] illuminaio_0.4.0 IRanges_1.20.6 iterators_1.0.6
[25] itertools_0.1-1 KernSmooth_2.23-10 lattice_0.20-24
[28] limma_3.18.7 locfit_1.5-9.1 MASS_7.3-29
[31] Matrix_1.1-0 matrixStats_0.8.12 mclust_4.2
[34] methylumi_2.8.0 mgcv_1.7-27 minfi_1.8.9
[37] multtest_2.18.0 nleqslv_2.1 nlme_3.1-113
[40] nor1mix_1.1-4 pkgmaker_0.17.4 preprocessCore_1.24.0
[43] R.methodsS3_1.5.2 RColorBrewer_1.0-5 RCurl_1.95-4.1
[46] registry_0.2 reshape_0.8.4 rngtools_1.2.3
[49] Rsamtools_1.14.2 rtracklayer_1.22.0 siggenes_1.36.0
[52] splines_3.0.2 stats4_3.0.2 stringr_0.6.2
[55] survival_2.37-4 tools_3.0.2 XML_3.95-0.2
[58] xtable_1.7-1 XVector_0.2.0 zlibbioc_1.8.0
Cheers,
Markus
--
DFCI Biostatistics & Computational Biology
Office Location: Center for Life Science Building, Room 11052
Phone: +1-617-582-7586
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
