Description Usage Arguments Value Author(s) References See Also Examples
Applies Sapirs and Churchills single slide method.
1 | stat.ChurSap(RG,layout,pp=0.95,norm="p", pout=TRUE, image.id=1,...)
|
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 |
pp |
Posterior probability of being differentially expressed. Defaults to 0.95 |
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"
|
pout |
if TRUE, an M vs. A plot will be produced with limits due to Churchill and Sapir at the specified posterior probability level. If FALSE, return a list with pertinant information |
... |
additional graphical parameters |
List containing the following components:
limits |
the positive value of the limit at the posterior probability value of pp |
theta |
parameters estimated by EM algorithm, specifically a mixing proportion and a variance |
pp |
Posterior probabilities of being differentially expressed given observed data for each gene. |
Ben Bolstad, bolstad@stat.berkeley.edu
Sapir and Churchill(2000), Estimating the posterior probability of differential gene expression from microarray data . http://www.jax.org/research/churchill/
1 2 3 4 | data(MouseArray)
##mouse.setup <- init.grid()
##mouse.data <- init.data() ## see \emph{init.data}
stat.ChurSap(mouse.data,mouse.setup,pp=0.95,image.id=3)
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