FindA0class: Class FindA0
Description
This is a class representation for the specification of the fudge factor
in an EBAM analysis as proposed by Efron et al. (2001).
Objects from the Class
Objects can be created using the function find.a0.Slots
mat.z:- Object of class
"matrix" containing the expression
scores of the genes for each of the possible values for the fudge factor,
where each row corresponds to a gene, and each column to one of the values
for the fudge factor $a0$. mat.posterior:- Object of class
"matrix" consisting of
the posterior probabilities of the genes for each of the possible values
for the fudge factor, where each row of mat.posterior corresponds to
a gene, and each column to one of the values for $a0$. The
probabilities in mat.posterior are computed using the monotonically
transformed test scores (see the Details section of find.a0). mat.center:- Object of class
"matrix" representing the
centers of the nrow(mat.center) intervals used in the logistic
regression with repeated observations for estimating $f/f0$
for each of the ncol(mat.center) possible values for the fudge
factor. mat.success:- Object of class
"matrix" consisting of
the numbers of observed test scores in the nrow(mat.success) intervals
used in the logistic regression with repeated observations for each
of the ncol(mat.success) possible values for the fudge factor. mat.failure:- Object of class
"matrix" containing the
numbers of permuted test scores in the nrow(mat.failure) intervals
used in the logistic regression with repeated observations for each
of the ncol(mat.failure) possible values for the fudge factor. z.norm:- Object of class
"numeric" comprising the
values of the nrow(mat.z) quantiles of the standard normal
distribution (if any mat.z<0< code="">) or an F-distribution (if all
mat.z >= 0). p0:- Object of class
"numeric" specifying the prior
probability that a gene is not differentially expressed. mat.a0:- Object of class
"data.frame" comprising
the number of differentially expressed genes and the estimated FDR
for the possible choices of the fudge factor specified by vec.a0. mat.samp:- Object of class
"matrix" consisting of the
nrow{mat.samp} permutations of the class labels. vec.a0:- Object of class
"numeric" representing the
possible values of the fudge factor $a0$. suggested:- Object of class
"numeric" revealing the
suggested choice for the fudge factor, i.e. the value of vec.a0
that leads to the largest number of differentially expressed genes. delta:- Object of class
"numeric" specifying the
minimum posterior probability that a gene must have to be called
differentially expressed. df.ratio:- Object of class
"numeric" representing the
degrees of freedom of the natural cubic spline used in the logistic
regression with repeated observations. msg:- Object of class
"character" containing information
about, e.g., the type of analysis. msg is printed when
print is 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 = "FindA0"): Generates a plot of the
(logit-transformed) posterior probabilities of the genes for a specified
value of $Delta$ and a set of possible values for the fudge
factor. For details, see help.finda0(plot). For
the arguments, see args.finda0(plot).- print
signature(object = "FindA0"): Prints the number of
differentially expressed genes and the estimated
FDR for each of the possible values of the fudge factor specified by
vec.a0. For details, see help.finda0(print).
For arguments, see args.finda0(print).- show
signature(object = "FindA0"): Shows the output of an
analysis with find.a0.
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.