EBAM-class {siggenes} | R Documentation

## Class EBAM

### 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, 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

`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)

[Package siggenes version 1.64.0 Index]