source("test/common.R")
library("Biobase")
library("biomaRt")
bottomly.eset <- load_bottomly()
bottomly.gene.names <- load_bottomly_gene_names(bottomly.eset)
counts <- exprs(bottomly.eset)
strain <- phenoData(bottomly.eset)$strain
experiment.number <- factor( phenoData(bottomly.eset)$experiment.number )
design <- model.matrix(~ strain + experiment.number)
labels <- paste0(substr(strain,1,1), experiment.number)
print(
varistran::shiny_report(
#y=varistran::vst(counts, method="anscombe.poisson"),
#y=varistran::vst(counts)[,],
counts=counts,
sample_labels=labels,
feature_labels=bottomly.gene.names))
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