read_cel_files = function(cel_files_path, chip_type, zipped){
if (chip_type %in% c("hgu133plus2", "hgu133a", "drosophila2")){
celFiles = affy::list.celfiles(cel_files_path, full = TRUE)
raw_data = affy::read.affybatch(filenames = celFiles)
} else if (chip_type %in% c("pd.huex.1.0.st.v2", "pd.hugene.2.0.st")){
celFiles = oligoClasses::list.celfiles( cel_files_path, full = TRUE, listGzipped = zipped)
raw_data = oligo::read.celfiles(filenames = celFiles)
} else {
message(c("Unknown Chip Type: ", chip_type))
stop()
}
#results
new("results",
raw_data = raw_data,
eset = ExpressionSet(),
topall = data.frame(),
volc_all = data.frame(),
cohorts_vec = NA_character_
)
}
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