## ----label='version', include=FALSE, cache=FALSE------------------------------
#suppressPackageStartupMessages(library(Biobase))
library(Biobase)
pkg.ver <- package.version("hgu133plus2CellScore")

## ----label='Setup', include=FALSE, cache=FALSE----------------------

## Save the current working directory
dir.main <- getwd()
## Set the name of the directory in which figures will be saved (if any)
dir.figures <- 'figures'

## global chunk options
library(knitr)
opts_chunk$set(
    concordance=FALSE,
    cashe=2,
    ## cache is only valid with a specific version of R and session info
    ## cache will be kept for at most a month (re-compute the next month)
    cache.extra=list(R.version,
                     sessionInfo(),
                     format(Sys.Date(), '%Y-%m')
                     ),
    autodep=TRUE,
    fig.path=paste0(dir.figures,"/"),
    tidy=FALSE,
    size="small",
    message=FALSE,
    warning=FALSE
)
options(width=70, promp="R> ", continue="+  ", useFancyQuotes=FALSE)

## ----eval=FALSE-----------------------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
#     install.packages("BiocManager")
# BiocManager::install()

## ----eval=FALSE-----------------------------------------------------
# BiocManager::install("hgu133plus2CellScore")

## ----eval=TRUE, echo=FALSE, cache=FALSE-----------------------------
options(BIOCINSTALLER_ONLINE_DCF=FALSE)

## ----eval=TRUE, echo=1:2, cache=FALSE, include=TRUE-----------------
library(Biobase)
library(hgu133plus2CellScore)

## ----eval=TRUE------------------------------------------------------
eset.std

## ----eval=FALSE-----------------------------------------------------
# ## Install affy
# if (!requireNamespace("BiocManager", quietly=TRUE))
#     install.packages("BiocManager")
# BiocManager::install("affy")
# ## Install YuGene
# install.packages("YuGene")
# 
# ## Load the packages
# library(affy)
# library(YuGene)
# 
# ## Read in all *.CEL files in the current working directory;
# ## if the files are not in the working directory then uncomment
# ## the first command line and then read the files. Note that
# ## path_to_CEL should be replaced with path to the directory
# ## containing the *.CEL files
# 
# #setwd(path_to_CEL)
# data <- ReadAffy()
# 
# ## Background noise correction
# bg.corr <- expresso(data, bg.correct=TRUE, bgcorrect.method="rma",
#                     normalize=FALSE, pmcorrect.method="pmonly",
#                     summary.method="avgdiff")
# ## Log2-transform the background corrected data
# bg.corr.log2 <- log2(bg.corr)
# ## Perform YuGene transform (that results with
# ## normalized expression values between 0 and 1)
# normalized.matrix <- YuGene(bg.corr.log2)
# 
# ## Calculate mas5 present/absent calls
# co <- mas5calls(data)
# co <- assayData(co)[["se.exprs"]] #extract detection p-values
# pvalue.detection.cutoff <- 0.05
# calls.matrix <- co < pvalue.detection.cutoff

## ----eval=FALSE-----------------------------------------------------
# ## Example code:
# ## Create a new assayData object from the normalized expression data
# ## and the calls matrix
# assay.data <- assayDataNew(exprs=as.matrix(normalizedSub.matrix),
#                            calls=as.matrix(callsSub.matrix) )
# ## Create an AnnotatedDataFrame object from the phenotype data frame
# pheno.table <- new("AnnotatedDataFrame", data=phenotype.data.frame)
# ## Create an AnnotatedDataFrame object from the annotation data frame
# annotation.table <- new("AnnotatedDataFrame", data=annotation.data.frame)
# ## Create the new ExpressionSet object with all the data in one object
# eset.std <- ExpressionSet(assayData=assay.data,
#                           phenoData=pheno.table,
#                           featureData=annotation.table)

## ----eval=TRUE, echo=TRUE-------------------------------------------
sessionInfo()