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{
  \item{x}{ An unnormalised AffyBatch object }
  \item{tau}{ Errrmmm... tau }
  \item{alpha1}{ Present-Marginal threshold }
  \item{alpha2}{ Marginal-Absent threshold }
  \item{calls}{ if true generate PMA calls }
  \item{ignore.saturated}{ if true do the saturation correction described in the paper, with a saturation level of 46000 }
}
\value{
  A list:
  \item{pval}{A matrix of detection p values}
  \item{call}{PMA calls}
}
\references{ http://bioinformatics.picr.man.ac.uk/ }
\author{ Crispin J Miller }

 ~Make other sections like Warning with \section{Warning }{....} ~ 

\note{
  Alpha1 and Alpha2 are parameters that change according to the chip type you are using. see this-is-escaped-code{ for more details.
}
\seealso{
  this-is-escaped-codenormal-bracket31bracket-normal
}
\examplesnormal-bracket34bracket-normal
   ## Not run: 
     dpv <- detection.p.val(eset);
   
## End(Not run)
  normal-bracket34bracket-normal

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

Warning

....

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 Contents]