Description Usage Arguments Value Author(s) References See Also Examples
Applies Newtons single slide method.
1 | stat.Newton(RG,layout,norm="p", image.id=1,pout=TRUE)
|
RG |
a list with 4 elements, each represents a matrix with p rows for p
genes and n columns for n slides. |
layout |
a list specifying the dimensions of the spot matrix and the grid
matrix. This can be generated by calling |
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"
|
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 |
List containing the following components:
theta |
parameters estimated by EM algorithm |
lod |
Log odds ratio of being differentially expressed for each gene |
Ben Bolstad, bolstad@stat.berkeley.edu
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
1 2 3 4 | data(MouseArray)
##mouse.setup <- init.grid()
##mouse.data <- init.data() ## see \emph{init.data}
stat.Newton(mouse.data,mouse.setup,image.id=3)
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