[Bioc-devel] GSVA and LumiBatch objects

[Robert Castelo]

hi again,

thanks for your patience, the problem below has been fixed in GSVA 
release and development versions 1.10.2 and 1.11.3, respectively. You 
can specifically update GSVA from R with the following two instructions:

library(BiocInstaller)
update.packages(oldPkgs="GSVA", repos=biocinstallRepos(), ask=FALSE)

note that when passing a LumiBatch object as input the output is going 
to be an ExpressionSet object because the resulting pathway-level 
summaries of expression have no distinctive features of the illumina 
platform. The phenotypic data in the LumiBatch object, however, will 
continue to be part of the resulting object.

cheers,
robert.

On 12/30/2013 10:11 PM, Markus Riester wrote:
> 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
>
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>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550