readCelfiles: Read '.CEL' files into a matrix
In oncoclass/hemaClass: One-by-one normalization and classification of hematological malignacies

Description Usage Arguments Details Value Author(s) References See Also Examples

Affymetrix .CEL files given in the argument filenames are read into a matrix in R.

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readCelfiles(filenames, cdfname = NULL, rm.mask = FALSE,
  rm.outliers = FALSE, rm.extra = FALSE, verbose = FALSE,
  which = c("pm", "mm", "both"))

`filenames`	File names in a character vector.
`cdfname`	Used to specify the name of an alternative cdf package. If set to `NULL`, then the usual cdf package based on Affymetrix' mappings will be used.
`rm.mask`	Should the spots marked as `'MASKS'` set to `NA`?
`rm.outliers`	Should the spots marked as `'OUTLIERS'` set to `NA`?
`rm.extra`	If `TRUE`, then overrides what is in `rm.mask` and `rm.oultiers`.
`verbose`	logical. Should file names be written as they are read into R.
`which`	A `character` determining if `pm`, `mm`, or `both` probes be stored in matrices.

Load .CEL files into a matrix.

Expression matrix consisting of all pm probes.

Steffen Falgreen <sfl (at) rn.dk>
Anders Ellern Bilgrau <abilgrau (at) math.aau.dk>

Reference to the hemaClass.com paper

For preprocessing of the cel files see rmaPreprocessing.

# Read hgu133plus2 .CEL files into R

files <- dir(system.file("extdata/celfiles", package = "hemaClass"),
             full.names = TRUE)
CEL.data <- readCelfiles(files)