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

In simpleaffy: Very simple high level analysis of Affymetrix data

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.

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.

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

Author(s)

Crispin J Miller

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)

simpleaffy documentation built on Nov. 8, 2020, 11:09 p.m.