z.ebam {siggenes} | R Documentation |
Computes the required statistics for an Empirical Bayes Analysis with a modified t- or F-test.
Should not be called directly, but via
ebam(..., method = z.ebam)
or find.a0(..., method = z.find)
,
respectively.
z.ebam(data, cl, a0 = NULL, quan.a0 = NULL, B = 100, var.equal = FALSE, B.more = 0.1, B.max = 30000, n.subset = 10, fast = FALSE, n.interval = 139, df.ratio = NULL, rand = NA) z.find(data, cl, B = 100, var.equal = FALSE, B.more = 0.1, B.max = 30000)
data |
a matrix, data frame or ExpressionSet object. Each row of x
(or exprs(x) ) must correspond to a gene, and each column to a sample |
cl |
a numeric vector of length ncol(x) containing the class
labels of the samples. For details on how cl should be specified,
see ebam |
a0 |
a numeric value specifying the fudge factor |
quan.a0 |
a numeric value between 0 and 1 specifying the quantile of the standard deviations of the genes that is used as fudge factor |
B |
an integer indicating how many permutations should be used in the estimation of the null distribution |
var.equal |
should the ordinary t-statistic assuming equal group variances
be computed? If FALSE (default), Welch's t-statistic will be computed |
B.more |
a numeric value. If the number of all possible permutations is smaller
than or equal to (1+B.more )*B , full permutation will be done.
Otherwise, B permutations are used. This avoids that B permutations
will be used – and not all permutations – if the number of all possible
permutations is just a little larger than B |
B.max |
a numeric value. If the number of all possible permutations is smaller
than or equal to B.max , B randomly selected permutations will be used
in the computation of the null distribution. Otherwise, B random draws
of the group labels are used. In the latter way of permuting, it is possible that
some of the permutations are used more than once |
n.subset |
an integer specifying in how many subsets the B permutations
should be split when computing the permuted test scores. Note that the meaning
of n.subset differs between the SAM and the EBAM functions |
fast |
if FALSE the exact number of permuted test scores that are
more extreme than a particular observed test score is computed for each of
the genes. If TRUE , a crude estimate of this number is used |
n.interval |
the number of intervals used in the logistic regression with repeated observations for estimating the ratio f0/f |
df.ratio |
integer specifying the degrees of freedom of the natural cubic spline used in the logistic regression with repeated observations |
rand |
integer. If specified, i.e. not NA , the random number generator
will be set into a reproducible state |
a list of object required by find.a0 or ebam, respectively
Holger Schwender, holger.schw@gmx.de
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.