detection.p.val: Calculate Detection p-values

In simpleaffy: Very simple high level analysis of Affymetrix data

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

Note

alpha1 and alpha2 are parameters that change according to the chip type you are using. If they are not specified, the function uses the current QC environment to find them, and attempts to set one up if it is not there. This is done with an internal call to the function setQCEnvironment. If it is unable to find the appropriate config files, this will cause an error. See setQCEnvironment for more details.

Author(s)

Crispin J Miller

References

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

See Also

setQCEnvironment

Examples

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

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