[Bioc-devel] GSVA and LumiBatch objects

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

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DFCI Biostatistics & Computational Biology
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