Description Objects from the Class Slots Methods Author(s) References See Also Examples

This is a class representation for the Empirical Bayes Analysis of Microarrays (EBAM) proposed by Efron et al. (2001).

Objects can be created using the function `ebam`

.

`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`""`

.

- 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)`

.`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)`

.

Holger Schwender, [email protected]

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ```
## 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)
``` |

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