FindA0class {siggenes} | R Documentation |
This is a class representation for the specification of the fudge factor in an EBAM analysis as proposed by Efron et al. (2001).
Objects can be created using the function find.a0
.
mat.z
:"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
:"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
:"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
:"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
:"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
:"numeric"
comprising the
values of the nrow(mat.z)
quantiles of the standard normal
distribution (if any mat.z<0
) or an F-distribution (if all
mat.z>=0
).p0
:"numeric"
specifying the prior
probability that a gene is not differentially expressed.mat.a0
:"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
:"matrix"
consisting of the
nrow{mat.samp}
permutations of the class labels.vec.a0
:"numeric"
representing the
possible values of the fudge factor a0.suggested
:"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
:"numeric"
specifying the
minimum posterior probability that a gene must have to be called
differentially expressed.df.ratio
:"numeric"
representing the
degrees of freedom of the natural cubic spline used in the logistic
regression with repeated observations.msg
:"character"
containing information
about, e.g., the type of analysis. msg
is printed when
print
is called.chip
:"character"
naming the microarray
used in the analysis. If no information about the chip is available,
chip
will be set to ""
.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)
.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)
.signature(object = "FindA0")
: Shows the output of an
analysis with find.a0
.Holger Schwender, holger.schw@gmx.de
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.