anovaint {OLIN} | R Documentation

## One-factorial ANOVA assessing intensity-dependent bias

### Description

This function performs an one-factorial analysis of variance assessing intensity-dependent bias for a single array. The predictor variable is the average logged intensity of both channels and the response variable is the logged fold-change.

### Usage

    anovaint(obj,index,N=10)

### Arguments

`obj` | object of class “marrayRaw” or “marrayNorm”
`index` | index of array to be tested
`N` | number of (intensity) levels for ANOVA

### Details

The function `anovaint` performs a one-factorial ANOVA for objects of class “marrayRaw” or “marrayNorm”. The predictor variable is the average logged intensity of both channels `A=0.5*(log2(Ch1)+log2(Ch2))`. `Ch1,Ch2` are the fluorescence intensities of channel 1 and channel 2, respectively. The response variable is the logged fold-change `M=(log2(Ch2)-log2(Ch1))`. The `A`-scale is divided in `N` intervals generating `N` levels of factor `A`. Note that `N` should divide the total number of spots approx. equally. The null hypothesis is the equality of `mean(M)` of the different levels (intervals). The model formula used is M ~ (A - 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 `A` (based on the chosen ANOVA model.)

### Author(s)

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

### See Also

`anova`, `summary.lm`, `anovaspatial`, `marrayRaw`, `marrayNorm`

### Examples

    # CHECK RAW DATA FOR INTENSITY-DEPENDENT BIAS
    data(sw)
    print(anovaint(sw,index=1,N=10))

    # CHECK  DATA NORMALISED BY OLIN FOR INTENSITY-DEPENDENT BIAS
    data(sw.olin)
    print(anovaint(sw.olin,index=1,N=10))

[Package OLIN version 1.6.0 Index]