anovaplate {OLIN} | R Documentation

## One-factorial ANOVA assessing pin-dependent bias

### Description

This function performs an one-factorial analysis of variance assessing microtiter plate-dependent bias for a single array

### Usage

    anovaplate(obj,index)

### Arguments

`obj` | object of class “marrayRaw” or “marrayNorm”
`index` | index of array to be tested

### Details

The function `anovapin` performs a one-factorial ANOVA for objects of class “marrayRaw” or “marrayNorm”. The predictor variable is the corresponding plate index as stored in the `maPlate` slot of `obj`; the response variable is the logged fold-change `M=(log2(Ch2)-log2(Ch1))`. The null hypothesis is equal `mean(M)` of groups of spots derived from the same microtiter plate i.e. a spot's M does not dependent on the plate of origin. The model formula used is M ~ (plate.index - 1) (without an intercept term).

### Value

The return value is a list of summary statistics of the fitted model as produced by `summary.lm`. For example, the squared multiple correlation coefficient R-square equals the proportion of the variation of `M` that can be explained by the variation of plate index (based on the chosen ANOVA model.)

### Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

### See Also

`anova`, `summary.lm`

### Examples

    # CHECK RAW DATA FOR INTENSITY-DEPENDENT BIAS
    data(sw)
    print(anovapin(sw,index=1))

    # CHECK  DATA NORMALISED BY OLIN FOR INTENSITY-DEPENDENT BIAS
    data(sw.olin)
    print(anovapin(sw.olin,index=1))

[Package OLIN version 1.3.2 Index]