Hi Markus,
we did not test GSVA with LumiBatch objects before and that's the reason
we did not encounter this problem. I've taken a brief look to the
definition of the LumiBatch class of objects and my understanding of it
is that it contains the ExpressionSet class, and therefore, all methods
for ExpressionSet objects should work with LumiBatch objects.
when the input to the gsva() function is an ExpressionSet objects,
internally, the matrix of -p genes by n sample- expression values is
extracted via the "exprs" method and at the end of the function the
input ExpressionSet object is copied and its pxn matrix of expression
values is replaced by the resulting sxn matrix (s being here the number
of gene sets) of gene set summaries of expression, via the "exprs<-"
replacement method for ExpressionSet objects.
as far as i can tell from my brief look to the source code of the lumi
package, where the LumiBatch class is defined, the "exprs" and "exprs<-"
methods are not specifically defined again for LumiBatch objects so, and
this should be the advantage of using S4 classes, everything should work
out of the box.
if i just try to do the steps the gsva() function does, which i
previously described, it does not work either outside the scope of the
gsva() function. Using your example:
library(lumi)
library(GSVA)
library(GSVAdata)
library(lumiHumanAll.db)
data(example.lumi)
data(c2BroadSets)
res.matrix <- gsva(exprs(example.lumi), c2BroadSets,
annotation=annotation(example.lumi))$es.obs
dim(res.matrix)
[1] 2986 4
res.eset <- example.lumi
exprs(res.eset) <- res.matrix
dim(res.eset)
Features Samples
8000 4
so, to me, since no error or warning is triggered and the result is not
correct, something it is not working at the level of the definition of
the replacement method for 'ExpressionSet' objects when the object is a
LumiBatch object.
i'm cc'ing Martin Morgan who may have a hint about how to resolve this.
cheers,
robert.
On 12/30/2013 10:11 PM, Markus Riester wrote:
Hi Justin,
GSVA does not work correctly with LumiBatch objects. It does all the
calculations, but then returns the original input data object, not the pathway
collapsed version of the input data.
library(lumi)
library(GSVA)
library(GSVAdata)
library(lumiHumanAll.db)
data(example.lumi)
data(c2BroadSets)
res.eset<- gsva(example.lumi, c2BroadSets)$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
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