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) 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.

Author(s)

Holger Schwender, holger.schw@gmx.de

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.

See Also

find.a0, ebam, EBAM-class

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