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siggenes (version 1.46.0)

ebam: Empirical Bayes Analysis of Microarrays

Description

Performs an Empirical Bayes Analysis of Microarrays (EBAM). It is possible to perform one and two class analyses using either a modified t-statistic or a (standardized) Wilcoxon rank statistic, and a multiclass analysis using a modified F-statistic. Moreover, this function provides a EBAM procedure for categorical data such as SNP data and the possibility to employ an user-written score function.

Usage

ebam(x, cl, method = z.ebam, delta = 0.9, which.a0 = NULL, control = ebamControl(), gene.names = dimnames(x)[[1]], ...)

Arguments

x
either a matrix, a data frame or an ExpressionSet object, or the output of find.a0, i.e.\ an object of class FindA0. Can also be a list (if method = chisq.ebam or method = trend.ebam). For the latter case, see chisq.ebam. If x is not a FindA0 object, then each row of x (or exprs(x), respectively) must correspond to a variable (e.g., a gene or a SNP), and each column to a sample.
cl
a specification of the class labels of the samples. Ignored if x is a FindA0 object. Needs not to be specified if x is a list. Typically, cl is specified by a vector of length ncol(x). In the two class paired case, cl can also be a matrix with ncol(x) rows and 2 columns. If x is an ExpressionSet object, cl can also be a character string naming the column of pData(x) that contains the class labels of the samples. In the one-class case, cl should be a vector of 1's. In the two class unpaired case, cl should be a vector containing 0's (specifying the samples of, e.g., the control group) and 1's (specifying, e.g., the case group). In the two class paired case, cl can be either a numeric vector or a numeric matrix. If it is a vector, then cl has to consist of the integers between -1 and $-n/2$ (e.g., before treatment group) and between 1 and $n/2$ (e.g., after treatment group), where $n$ is the length of cl and $k$ is paired with $-k$, $k=1,\dots,n/2$. If cl is a matrix, one column should contain -1's and 1's specifying, e.g., the before and the after treatment samples, respectively, and the other column should contain integer between 1 and $n/2$ specifying the $n/2$ pairs of observations. In the multiclass case and if method = chisq.ebam or method = trend.ebam, cl should be a vector containing integers between 1 and $g$, where $g$ is the number of groups. In the two latter cases, cl needs not to be specified, if x is a list. For details, see chisq.ebam. For examples of how cl can be specified, see the manual of siggenes.
method
a character string or name specifying the method or function that should be used in the computation of the expression score $z$. If method = z.ebam, a modified t- or F-statistic, respectively, will be computed as proposed by Efron et al. (2001). If method = wilc.ebam, a (standardized) Wilcoxon sum / signed rank statistic will be used as expression score. For an analysis of categorical data such as SNP data, method can be set to chisq.ebam. In this case, Pearson's Chi-squared statistic is computed for each row. If the variables are ordinal and a trend test should be applied (e.g., in the two-class case, the Cochran-Armitage trend test), method = trend.ebam can be employed. It is also possible to employ an user-written function for computing an user-specified expression score. For details, see the vignette of siggenes.
delta
a numeric vector consisting of probabilities for which the number of differentially expressed genes and the FDR should be computed, where a gene is called differentially expressed if its posterior probability is larger than $Delta$.
which.a0
an integer between 1 and the length of quan.a0 of find.a0. If NULL, the suggested choice of find.a0 is used. Ignored if x is a matrix, data frame or ExpressionSet object.
control
further arguments for controlling the EBAM analysis. For these arguments, see ebamControl.
gene.names
a vector of length nrow(x) specifying the names of the variables. By default, the row names of the matrix / data frame comprised by x are used.
...
further arguments of the specific EBAM methods. If method = z.ebam, see z.ebam. If method = wilc.ebam, see wilc.ebam. If method = chisq.ebam, see chisq.ebam.

Value

An object of class EBAM.

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. (2006). Identifying Interesting Genes with siggenes. RNews, 6(5), 45-50. Storey, J.D. and Tibshirani, R. (2003). Statistical Significance for Genome-Wide Studies. Proceedings of the National Academy of Sciences, 100, 9440-9445.

See Also

EBAM-class, find.a0, z.ebam, wilc.ebam, chisq.ebam