Description Usage Arguments Details Value Author(s) References See Also
Specifies most of the optional arguments of sam
.
1 2 | samControl(delta = NULL, n.delta = 10, p0 = NA, lambda = seq(0, 0.95, 0.05),
ncs.value = "max", ncs.weights = NULL, q.version = 1)
|
delta |
a numeric vector specifying a set of values for the threshold
Delta that should be used. If |
n.delta |
a numeric value specifying the number of Delta values
that will be computed over the range of all possible values for Delta
if |
p0 |
a numeric value specifying the prior probability pi0
that a gene is not differentially expressed. If |
lambda |
a numeric vector or value specifying the lambda
values used in the estimation of the prior probability. For details, see
|
ncs.value |
a character string. Only used if |
ncs.weights |
a numerical vector of the same length as |
q.version |
a numeric value indicating which version of the q-value should
be computed. If |
These parameters should only be changed if they are fully understood.
A list containing the values of the parameters that are used in sam
.
Holger Schwender, holger.schwender@udo.edu
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.
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
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