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.
1 2 3 4 5 6 |
data |
a matrix, data frame or ExpressionSet object. Each row of |
cl |
a numeric vector of length |
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 |
B.more |
a numeric value. If the number of all possible permutations is smaller
than or equal to (1+ |
B.max |
a numeric value. If the number of all possible permutations is smaller
than or equal to |
n.subset |
an integer specifying in how many subsets the |
fast |
if |
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 |
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.
ebam
, find.a0
, d.stat
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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