stat.Newton {sma}R Documentation

Apply Newtons single slide method

Description

Applies Newtons single slide method.

Usage

stat.Newton(RG,layout,norm="p", image.id=1,pout=TRUE)

Arguments

RG a list with 4 elements, each represents a matrix with p rows for p genes and n columns for n slides.
The first element "R" contains the raw red intensities from slide i=1,...,n .
Similarly, the second element "G" contains the raw green intensities.
The third element "Rb" contains the background red intensities and
the fourth element "Gb" contains the background green intensities.
This list structure can be generated by the interactive function init.data.
layout a list specifying the dimensions of the spot matrix and the grid matrix. This can be generated by calling init.grid.
norm Character string, one of "n", "m", "l", "p" or "s". This argument specifies the type of normalization method to be performed: "n" no normalization between the 2 channels; "m" median normalization, which sets the median of log intensity ratios to zero; "l" global lowess normalization; "p" print-tip group lowess normalization and "s" scaled print-tip group lowess normalization. The default method is set to print-tip normalization.
image.id Specifies image to which Chen's method will be applied.
pout if TRUE, an M vs. A plot will be produced with limits due to Newton, Specifically limits at the 1:1, 1:10 and 1:100 log odds ratio. If FALSE, return a list with pertinant information

Value

List containing the following components:

theta parameters estimated by EM algorithm
lod Log odds ratio of being differentially expressed for each gene

Author(s)

Ben Bolstad, bolstad@stat.berkeley.edu

References

Newton, M.N., C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui . On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. Technical Report 139, Department of Biostatistics and Medical Informatics, UW Madison, 1999. http://www.stat.wisc.edu/~newton/papers/abstracts/btr139a.html

See Also

stat.Chen,stat.ChurSap

Examples

data(MouseArray)
##mouse.setup <- init.grid() 
##mouse.data <- init.data() ## see \emph{init.data}
stat.Newton(mouse.data,mouse.setup,image.id=3)

[Package sma version 0.5.15 Index]