EBAM-class: Class EBAM

In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

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).

Author(s)

Holger Schwender, [e-mail]

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

ebam, find.a0, FindA0-class

Examples

## Not run: 
  # Load the data of Golub et al. (1999) contained in the package multtest.
  data(golub)
  
  # golub.cl contains the class labels.
  golub.cl
  
  # Perform an EBAM analysis for the two class unpaired case assuming
  # unequal variances. Specify the fudge factor a0 by the suggested
  # choice of find.a0
  find.out <- find.a0(golub, golub.cl, rand = 123)
  ebam.out <- ebam(find.out)
  ebam.out
    
  # Obtain the number of differentially
  # expressed genes and the FDR if a gene is called differentially
  # expressed if its posterior probability is larger than 0.8, 0.85,
  # 0.9, 0.95.
  print(ebam.out, c(0.8, 0.85, 0.9, 0.95))
    
  # Generate a plot of the posterior probabilities for delta = 0.9.
  plot(ebam.out, 0.9)
    
  # Obtain the list of genes called differentially expressed if their
  # posterior probability is larger than 0.99, and gene-specific 
  # statistics for these variables such as their z-value and their
  # local FDR.
  summary(ebam.out, 0.9)
  

## End(Not run)

siggenes documentation built on Nov. 8, 2020, 6:26 p.m.