detection.p.val {simpleaffy}R Documentation

Calculate Detection P Values

Description

Calculate detection p values and Present Marginal Absent calls, a la MAS5.0. This is an implementation based on the algorithm described in Liu, Mei et al. (2002) 'Analysis of high density expression microarrays with signed-rank call algorimths', Bioinformatics 18(12) pp1593-1599.

Usage

detection.p.val(x, tau = 0.015,calls=TRUE,alpha1=getAlpha1(cleancdfname(cdfName(x))),alpha2=getAlpha2(cleancdfname(cdfName(x))),ignore.saturated=TRUE)

Arguments

x An unnormalised AffyBatch object
tau Errrmmm... tau
alpha1 Present-Marginal threshold
alpha2 Marginal-Absent threshold
calls if true generate PMA calls
ignore.saturated if true do the saturation correction described in the paper, with a saturation level of 46000

Value

A list:

pval A matrix of detection p values
call PMA calls

Note

Alpha1 and Alpha2 are parameters that change according to the chip type you are using. see getQCParams for more details.

Author(s)

Crispin J Miller

References

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

See Also

getQCParams

Examples

   ## Not run: 
     dpv <- detection.p.val(eset);
   
## End(Not run)

[Package simpleaffy version 2.4.2 Index]