Download data from array express + create expressionset object

Script

setwd(datadirectory)
#library("Biobase")
library(ArrayExpress)
#####################################################################################
###get the dataset from the ArrayExpress website 
#####################################################################################
#setwd(datadirectory)
#library(ArrayExpress)
data_ae <- getAE(arrayfile, type="processed")
files<-data_ae
path = files$path

R Server

Script

#This dataset contains two processed files, one from each array. To get the expression values from array A we need to  indicate in the command
#files$processedFiles[1],  for array B -> files$processedFiles[2]
procfile_a = files$processedFiles[array_number]
coln = scan(file.path(path, procfile_a), what = "", nlines = 1,skip = 1, sep = "\t")
cn=unique(coln)
procol_a<-cn[3]


proctot_a = read.table(file.path(path, procfile_a), header = TRUE,sep = "\t", quote = "", row.names = 1,  check.names=FALSE)
procsel_a = matrix(as.numeric(as.matrix(proctot_a[-1, procol_a == proctot_a[1, ]])), nrow = nrow(proctot_a) - 1)
procsel_a = log2(procsel_a)
colnames(procsel_a) = colnames(proctot_a[, procol_a == proctot_a[1,]])
rownames(procsel_a) = rownames(proctot_a[-1, ])
proceset_a = new("ExpressionSet", exprs = procsel_a)
ph_a = try(read.AnnotatedDataFrame(files$sdrf, path = path, row.names = NULL,blank.lines.skip = TRUE, fill = TRUE,varMetadata.char = "$"))
phenoData(proceset_a) = ph_a
idx_a<-match(colnames(exprs(proceset_a )) , pData(proceset_a)$Hybridization.Name)
phenoData(proceset_a) = ph_a[idx_a]
probe_ids<-rownames(exprs(proceset_a))

#out1<-"expression set object done"
#probes<-probe_ids
write.table(exprs(proceset_a),"gene_expression.txt", col.names=TRUE, row.names=TRUE,sep="\t" )
write.table(pData(proceset_a), "phenodata.txt",col.names=TRUE, row.names=FALSE,sep="\t") 

R Server