anovapin {OLIN}R Documentation

One-factorial ANOVA assessing pin-dependent bias

Description

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

Usage

anovapin(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 pin index; the response variable is the logged fold-change M=(log2(Ch2)-log2(Ch1)). The null hypothesis is equal mean(M) of groups of spots printed by the same pin i.e. a spot's M does not dependent on the pin used from printing the spot. The model formula used is M ~ (pin.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 pin 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]