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- ## Load packages
- library(openxlsx)
- library(affy)
- library(frma)
- ## Load the fRMA data package and then load the data
- library(DSalomon.PAX.hthgu133pluspmfrmavecs)
- data(DSalomon.PAX.hthgu133pluspmfrmavecs)
- ## Get the sample table and list of CEL files
- cel.dir <- "Training Data/01 - CTOT08 ABECASSIS PAX Samples"
- ## Read the first xlsx file in the directory, which is a spreadsheet
- ## containing all of the CEL file names
- sample.table <- read.xlsx(list.files(cel.dir, pattern=glob2rx("*.xlsx"), full.names=TRUE)[1])
- cel.files <- file.path(cel.dir, sample.table$Filename)
- ## Read the data from the CEL files
- affy <- ReadAffy(filenames=cel.files, phenoData=sample.table)
- ## Apply fRMA
- eset <- frma(affy, input.vecs=DSalomon.PAX.hthgu133pluspmfrmavecs)
- ## Extract expression matrix
- expr <- exprs(eset)
- ## Extract sample table
- sample.table <- pData(eset)
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