## list of ExpressionSets
data("sample.ExpressionSet") ## from Biobase
es.list <- list( sample.ExpressionSet[,1:4],
sample.ExpressionSet[,5:8],
sample.ExpressionSet[,9:12])
names(es.list) <- paste( "Instance", 1:3, sep=".")
de <- generate_gCMAP_NChannelSet(
es.list,
1:3,
platform.annotation = annotation(es.list[[1]]),
control_perturb_col="type",
control="Control",
perturb="Case")
assayDataElementNames(de)
head( assayDataElement(de, "z") )
## Not run:
# ## processing RNAseq data requires the suggested 'DESeq'
# ## Bioconductor package.
# require( DESeq )
# set.seed( 123 )
# ## list of CountDataSets
# cds.list <- lapply( 1:3, function(n) {
# cds <- makeExampleCountDataSet()
# featureNames(cds) <- paste("gene",1:10000, sep="_")
# cds
# })
#
# cde <- generate_gCMAP_NChannelSet(cds.list,
# uids=1:3,
# sample.annotation=NULL,
# platform.annotation="Entrez",
# control_perturb_col="condition",
# control="A",
# perturb="B")
#
# assayDataElementNames(cde)
# ## End(Not run)
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