Description
This is a class representation for the Empirical Bayes Analysis of
Microarrays (EBAM) proposed by Efron et al. (2001).
Objects from the Class
Objects can be created using the function ebam.Slots
z:- Object of class
"numeric" representing the
expression scores of the genes. posterior:- Object of class
"numeric" representing
the posterior probabilities of the genes. p0:- Object of class
"numeric" specifying the
prior probability that a gene is not differentially expressed. local:- Object of class
"numeric" consisting of the
local FDR estimates for the genes. mat.fdr:- Object of class
"matrix" containing general
statistics such as the number of differentially expressed genes and
the estimated FDR for the specified values of delta. a0:- Object of class
"numeric" specifying the used
value of the fudge factor. If not computed, a0 will be
set to numeric(0). mat.samp:- Object of class
"matrix" containing
the permuted group labels used in the estimation of the null
distribution. Each row represents one permutation, each column
one observation (pair). If no permutation procedure has been used,
mat.samp will be set to matrix(numeric(0)). vec.pos:- Object of class
"numeric" consisting of
the number of positive permuted test scores that are absolutely
larger than the test score of a particular gene for each gene.
If not computed vec.pos is set to numeric(0). vec.neg:- Object of class
"numeric" consisting of
the number of negative permuted test scores that are absolutely
larger than the test score of a particular gene for each gene.
If not computed vec.neg is set to numeric(0). msg:- Object of class
"character" containing information
about, e.g., the type of analysis. msg is printed when the functions
print and summary are called. chip:- Object of class
"character" naming the microarray
used in the analysis. If no information about the chip is available,
chip will be set to "".
Methods
- plot
signature(object = "EBAM"): Generates a plot of the
posterior probabilities of the genes for a specified value of
$Delta$. For details, see help.ebam(plot). For
the arguments, see args.ebam(plot).- print
signature(object = "EBAM"): Prints general information
such as the number of differentially expressed genes and the estimated
FDR for several values of $Delta$. For details, see
help.ebam(print). Arguments can be listed by args.ebam(print).- show
signature(object = "EBAM"): Shows the output of an
EBAM analysis.- summary
signature(object = "EBAM"): Summarizes the results
of an EBAM analysis for a specified value of $Delta$.
For details, see help.ebam(summary). For the arguments,
see args.ebam(summary).
References
Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis
of a Microarray Experiment, JASA, 96, 1151-1160.
Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of
the Empirical Bayes and the Significance Analysis of Microarrays.
Technical Report, SFB 475, University of Dortmund, Germany.