fdr {MIMOSA} | R Documentation

## Compute the fdr (q-value) from posterior probabilities

### Description

Given the z's from a MIMOSA model, calculates the q-values for each observation.

### Usage

    fdr(z)

    ## S3 method for class 'matrix'
    fdr(z)

    ## S3 method for class 'MIMOSAResult'
    fdr(z)

    ## S3 method for class 'MIMOSAResultList'
    fdr(z)

### Arguments

`z` | matrix of posterior probabilties, or a `MIMOSAResult`, or `MIMOSAResultList`

### Value

a vector of q-values or a list of vectors of q-values.

### Examples

    data(ICS)
    E<-ConstructMIMOSAExpressionSet(ICS,
                                  reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
                                   other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
                                   default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
                                   .variables=.(TCELLSUBSET,CYTOKINE,UID),
                                   featureCols=1,ref.append.replace='_REF')
    result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
       data=E, method='EM',
       subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
       ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
    qvalues<-fdr(result)

[Package MIMOSA version 1.20.1 Index]