gtypeCelToPQ: Function to immitate Affymetrix' gtype\_cel\_to\_pq software
In aroma.apd: A probe-level data file format used by aroma.affymetrix [DEPRECATED]

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

Function to immitate Affymetrix' gtype\_cel\_to\_pq software.

1 2	## Default S3 method: gtypeCelToPQ(filename, units=NULL, ..., cdf=NULL, nbrOfQuartets=NULL, verbose=FALSE)

`filename`	The name of a CEL file.
`units`	Indices of CDF units to be returned.
`...`	Arguments passed to `readCelUnits`.
`cdf`	A CDF `list` structure, the pathname of the CDF file, or `NULL`. If `NULL`, the CDF file corresponding to the chip type of the CEL file is searched for using `findCdf`.
`nbrOfQuartets`	The number of probe quartets in the returned `matrix`.
`verbose`	See `Verbose`.

Returns an NxK matrix where N is the number of probesets (SNPs) and K=4*Q where Q is the number of probe quartets (PMA,MMA,PMB,MMB). The rownames corresponds to the probeset names.

Henrik Bengtsson

[1] Affymetrix, Understanding Genotyping Probe Set Structure, 2005. http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx

gtypeCelToPQ(). applyCdfGroups.

# Scan for CEL files
files <- list.files(pattern="[.](cel|CEL)$")

# Convert each to RAW file
for (file in files) {
  rawFile <- gsub("[.][^.]*$", ".raw", file)
  file.remove(rawFile)
  cel <- gtypeCelToPQ(file, verbose=TRUE)
  write.table(file=rawFile, cel, sep="\t", quote=FALSE)
}