FindA0class {siggenes} | R Documentation

## 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`

[Package siggenes version 1.64.0 Index]