Description Usage Arguments Value Note Author(s) References See Also Examples
Computes the log intensity ratio M = log_2 (R/G) and the mean log intensity A = log_2(R*G)/2, where R and G represent the fluorescence intensities in the red and green channels, respectively. Logarithms base 2 are used instead of natural or decimal logarithms as intensities are typically integers between 1 and 2^{16}. The log intensity ratios M are normalized using one of the five available methods.
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 |
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. Otherwise, a matrix of log intensity ratios and average log intensities is return. By default pout is set to FALSE. The option pout='TURE' is not yet implemented. |
... |
other parameters used in |
List containing the following components:
M |
Matrix of log expression ratios M = log_2 (R/G) |
A |
Matrix of average log intensities A = log_2(R*G)/2 |
For the matrix in each of the components, rows correspond to genes and columns correspond to different hybridizations, that is different slides.
ma.func
, norm.l.func
,
norm.scale.func
and norm.pin.func
are called by stat.ma
and are not typically used on their own.
Yee Hwa Yang, yeehwa@stat.berkeley.edu
Sandrine Dudoit, sandrine@stat.berkeley.edu
Natalie Roberts, nroberts@wehi.edu.au
S. Dudoit, Y. H. Yang, M. J. Callow, and T. P. Speed. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments (Statistics, UC Berkeley, Tech Report \# 578).
ma.func
, norm.l.func
,
norm.pin.func
, norm.scale.func
, plot.mva
, lowess
.
1 2 3 4 | data(MouseArray)
## mouse.setup <- init.grid()
## mouse.data <- init.data() ## see \emph{init.data}
mouse.lratio <- stat.ma(mouse.data, mouse.setup)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.