detection.p.val {simpleaffy} | R Documentation |
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.
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
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 |
A list:
pval |
A matrix of detection p values |
call |
PMA calls |
....
Alpha1 and Alpha2 are parameters that change according to the chip type you are using. see getQCParams
for more details.
Crispin J Miller
http://bioinformatics.picr.man.ac.uk/
## Not run: dpv <- detection.p.val(eset); ## End(Not run)