tmixture {limma} | R Documentation |
This function estimates the unscaled standard deviation of the log fold change for differentially expressed genes.
It is called by the function ebayes
and is not intended to be called by users.
tmixture.vector(tstat,stdev.unscaled,df,proportion,v0.lim=NULL) tmixture.matrix(tstat,stdev.unscaled,df,proportion,v0.lim=NULL)
tstat |
numeric vector or matrix of t-statistics |
stdev.unscaled |
numeric matrix conformal with tstatf containing the unscaled standard deviations for the coefficient estimators |
df |
numeric vector giving the degrees of freedom associated with tstat |
proportion |
assumed proportion of genes which are differentially expressed |
v0.lim |
numeric vector of length 2, assumed lower and upper limits for the estimated unscaled standard deviation |
The values in each column of tstat
are assumed to follow a mixture of an ordinary t-distribution, with mixing proportion 1-proportion
, and (v0+v1)/v1
times a t-distribution, with mixing proportion proportion
.
Here v1=stdev.unscaled^2
and v0
is the value to be estimated.
Numeric vector of length equal to the number of columns of tstat
and stdev.unscaled
.
Gordon Smyth