### Allie provided

source("http://bioconductor.org/biocLite.R")

#LOAD DATABASE AND AFFY LIBRARY

biocLite("ath1121501.db")

biocLite("affy")

biocLite("biobase")

#USE AFFY LIBRARY

require(affy)

#READ FILES

Data <- ReadAffy()

pData(Data)

#make a boxplot to look at the data

boxplot(Data)

#load phenodata file

pd <- read.AnnotatedDataFrame("Gifford_CELfilestokeep_PhenoData.txt")

phenoData(Data) <- pd

pData(pd)

#normalize data

nData <- rma(Data)

#look at normalized data

boxplot(exprs(nData),main="normalized data")

tnData <- t(as.data.frame(nData))

##write.csv(tnData, file="tnData.csv")

head(tnData)

#remove genes that are not expressed - threshold based per dataset

lowExprThresh = 6

rmvRows = apply (tnData, 1, function(x){all( x < lowExprThresh)})

enData = tnData[!rmvRows,]

write.csv(enData, file="Treatment_tnData_NOV26.csv")