stat.bayesian {sma} | R Documentation |
This function takes the normalized expression estimates from a multi-slide microarray experiment (M-values output by stat.ma) and returns an odds ratio for each gene: log( Pr(the gene is differentially expressed) / Pr(the gene is not differentially expressed) ). The parameter estimates of the Bayesian model used, as well as some data structures which are useful when presenting the lodscore graphically are also in the output.
stat.bayesian(X=NULL, nb=NULL, nw=1, Xprep=NULL, para=list(p = 0.01, v = NULL, a = NULL, c = NULL, k = NULL))
X |
List containing matrix of (normalized) log expression ratios M = log_2 (R/G) (E.g. output from stat.ma()) |
nb |
Number of slides containing spots for a gene (common for all genes). Unnecessary argument if nw=1. |
nw |
Number of spots for a gene within each slide (common to all genes).Default is 1. |
Xprep |
Some data structures useful in graphical presentation. (This is calculated only if not already supplied as input. See details!) |
para |
Estimates of the parameters used in the Bayesian calculations. (These are calculated only if not already supplied as input. See details!) |
A list of
Xprep |
Some data structures useful in graphical presentation. See details! |
para |
Estimates of the parameters used in the Bayesian calculations. See details! |
lods |
The log odds ratio for each gene. |
Ingrid Lönnstedt ingrid@math.uu.se
Yee Hwa Yang, yeehwa@stat.berkeley.edu
data(MouseArray) ## mouse.setup <- init.grid() ## mouse.data <- init.data() ## see \emph{init.data} ## mouse.lratio <- stat.ma(mouse.data, mouse.setup) ## mouse.bayesian<-stat.bayesian(X=mouse.lratio) ## plot(mouse.bayesian$Xprep$Mbar, mouse.bayesian$lods)