postProbNull {OVESEG} | R Documentation

## Posterior probabilities of each component null hypothesis

### Description

This function computes posterior probabilities of each component null hypothesis given observed probes. Such probe-wise probabilities will be used as weights for aggregating permutations.

### Usage

    postProbNull(y, group, weights = NULL, alpha = "moderated",
      detail.return = TRUE)

### Arguments

`y` | a numeric matrix containing log-expression or logCPM (log2-counts per million) values. Data frame or SummarizedExperiment object will be internally coerced into a matrix. Rows correspond to probes and columns to samples. Missing values are not permitted.
`group` | categorical vector or factor giving group membership of columns of y. At least two categories need to be presented.
`weights` | optional numeric matrix containing prior weights for each spot.
`alpha` | parameter specifying within-group variance estimator to be used. 'moderated': empirical Bayes moderated variance estimator as used in `eBayes`. Numeric value: a constant value added to pooled variance estimator (α + σ). NULL: no estimator; all variances are set to be 1.
`detail.return` | a logical indicating whether more details (e.g. lfdr) will be returned.

### Details

Posterior probabilities of each component null hypothesis given observed probes are estimated from ANOVA test on certain groups and local fdr. There are totally (K-1) null hypotheses, where K is the number of groups.

### Value

a list containing the following components:

`W` | a matrix of posterior probabilities for each component null hypothesis given an observed probe. Rows correspond to probes and columns to one hypothesis.
`label` | a vector of group labels.
`groupOrder` | a matrix with each row being group indexes ordered based on decreasing expression levels. Group indexes are positions in `label`.
`F.p.value` | a matrix with each column giving p-values corresponding to F-statistics on certain groups.
`lfdr` | a matrix with each column being local false discovery rates estimated based on one column of weighted F.p.value matrix.
`fit` | a `MArrayLM` fitted model object produced by `lmFit`.

`F.p.value`, `lfdr` and `fit` are returned only when `detail.return` is TRUE.

### Examples

    data(RocheBT)
    ppnull <- postProbNull(RocheBT$y, RocheBT$group, alpha='moderated')
    ppnull <- postProbNull(RocheBT$y, RocheBT$group, alpha=0.1)

[Package OVESEG version 1.2.0 Index]