importFromDChip.AffymetrixCelSet: Imports dChip-exported CEL files

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Imports dChip-exported CEL files

Description

Imports dChip-exported CEL files into a directory structure recognized by this package. ASCII CEL files are converted to binary CEL files, and for chip types where the array data is rotated 90-degrees counter clockwise by dChip, the data is rotated back.

As of 2007-03-28, dChip rotates data for exon, tiling, and Mapping 500K arrays.

Usage

## Static method (use this):
## AffymetrixCelSet$importFromDChip(path, name=NULL, tags="dChip", rootPath="probeData",
##   rotateBack=NA, ..., skip=TRUE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'AffymetrixCelSet'
importFromDChip(static, path, name=NULL, tags="dChip", rootPath="probeData",
  rotateBack=NA, ..., skip=TRUE, verbose=FALSE)

Arguments

path	The path to all dChip-exported CEL files.
name	The name of the output data set. If NULL, the name is inferred from the source path.
tags	Tags added to the imported data set.
rootPath	The root path where to store the data set.
rotateBack	If TRUE, the dChip-rotated array data is rotated back. If NA, this is inferred from the chip type name.
...	Additional arguments passed to byPath().
skip	If TRUE, already converted files are not re-converted.
verbose	See Verbose.

Details

Note that dChip stores CEL intensities as 16-bit integers in its *.dcp files, although CEL files are capable or holding floats. This means that you might loose precision if first import data in to dChip and then export it data again.

Value

Returns an AffymetrixCelSet.

Author(s)

Henrik Bengtsson

See Also

For more information see AffymetrixCelSet.

aroma.affymetrix documentation built on May 29, 2024, 4:32 a.m.