simpleaffy (version 2.48.0)

detection.p.val: Calculate Detection p-values

Description

Calculate MAS5 detection pvalues and Present Marginal Absent calls. 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 algorithms', Bioinformatics 18(12) pp1593-1599.

Usage

detection.p.val(x, tau = NULL,calls=TRUE,alpha1=NULL,alpha2=NULL,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

A matrix of PMA calls

References

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

See Also

setQCEnvironment

Examples

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