[Bioc-devel] GSVA and LumiBatch objects

[Markus Riester]

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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