simpleaffy (version 2.48.0)

justMAS: Generate Expression calls using a C implementation of the MAS 5.0 Algorithm

Description

Implements the MAS5.0 background correction, expression summary and scaling functions as described in Affy's 'Statistical Algorithms Description Document'

Usage

justMAS(unnormalised,tgt=100,scale=TRUE)

Arguments

unnormalised

An unnormalised AffyBatch object

tgt

The target intensity to scale array to, if scaling.

scale

Scale the data to the specified target intensity.

Value

An AffyBatch object, with, in addition, scale-factors for each array stored in the object's description@preprocessing@sfs slot, and the target intensity the arrays were scaled to in description@preprocessing@tgt

Details

Uses a C code implementation of the MAS5.0 algorithm (As described in Affymetrix's 'Statistical Algorithms Reference Guide' - see http://www.affymetrix.com, and in Hubbell et al. (2002) Robust Estimators for expression analysis. Bioinformatics 18(12) 1585-1592). Note that this function returns log2 data.

References

http://bioinformatics.picr.man.ac.uk/

See Also

http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf

Examples

   ## Not run: 
#      eset.mas <- justMAS(eset.mas);    
#    ## End(Not run)