stat.Chen {sma}R Documentation

Apply Chen's single slide method

Description

Applies Chens single slide method.

Usage

stat.Chen(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.
image.id Specifies image to which Chen's method will be applied.
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.
pout if TRUE, an M vs. A plot will be produced with limits due to Chen 95% and 99%. If FALSE, returns upper and lower bounds at 95% and 99% levels.

Value

List containing the following components:

lower01 The lower limit of 99% confidence interval
upper01 The upper limit of 99% confidence interval
lower05 The lower limit of 95% confidence interval
upper05 The upper limit of 95% confidence interval

Author(s)

Ben Bolstad, bolstad@stat.berkeley.edu

References

Chen, Y., E.R. Dougherty, and M.L. Bittner. Ratio-based decisions and the quantitative analysis of cDNA microarray images. Journal of Biomedical Optics , Volume 2 (4), 364-374, 1997. (1997)

See Also

stat.ChurSap,stat.Newton

Examples

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

[Package sma version 0.5.15 Index]