EBAM and SAM for Fuzzy Genotype Calls
Description
Computes the required statistics for an Empirical Bayes Analysis of Microarrays (EBAM; Efron et al., 2001) or a Significant Analysis of Microarrays (SAM; Tusher et al., 2001), respectively, based on the score statistic proposed by Louis et al. (2010) for fuzzy genotype calls or approximate Bayes Factors (Wakefield, 2007) determined using this score statistic.
Should not be called directly, but via ebam(..., method = fuzzy.ebam)
or sam(..., method = fuzzy.stat)
, respectively.
Usage
1 2 3 4 5 6 7 8  fuzzy.ebam(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL,
logbase = exp(1), addOne = TRUE, df.ratio = NULL, n.interval = NULL,
df.dens = 5, knots.mode = TRUE, type.nclass = c("FD", "wand", "scott"),
fast = FALSE, B = 100, B.more = 0.1, B.max = 30000, n.subset = 10, rand = NA)
fuzzy.stat(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL,
logbase = exp(1), addOne = TRUE, B = 100, B.more = 0.1, B.max = 30000,
n.subset = 10, rand = NA)

Arguments
data 
a matrix containing fuzzy genotype calls. Such a matrix can, e.g., be generated by the function

cl 
a vector of zeros and ones specifying which of the columns of 
type 
a character string specifying how the analysis should be performed. If 
W 
the prior variance. Must be either a positive value or a vector of length 
logbase 
a numeric value larger than 1. If 
addOne 
should 1 be added to the ABF before it is logtransformed? If 
df.ratio 
integer specifying the degrees of freedom of the natural cubic
spline used in the logistic regression with repeated observations for estimating the ratio f0/f. Ignored
if 
n.interval 
the number of intervals used in the logistic regression with
repeated observations (if 
df.dens 
integer specifying the degrees of freedom of the natural cubic
spline used in the Poisson regression to estimate the density of the observed
zvalues in an application of 
knots.mode 
logical specifying whether the 
type.nclass 
character string specifying the procedure used to compute the
number of cells of the histogram. Ignored if 
fast 
if 
B 
the number of permutations used in the estimation of the null distribution,
and hence, in the computation of the expected zvalues. Ignored 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 
a numeric value indicating in how many subsets the 
rand 
numeric value. If specified, i.e. not 
Value
A list containing statistics required by ebam
or sam
.
Author(s)
Holger Schwender, holger.schw@gmx.de
References
Efron, B., Tibshirani, R., Storey, J.D., and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 11511160.
Louis, T.A., Carvalho, B.S., Fallin, M.D., Irizarry, R.A., Li, Q., and Ruczinski, I. (2010). Association Tests that Accommodate Genotyping Errors. In Bernardo, J.M., Bayarri, M.J., Berger, J.O., Dawid, A.P., Heckerman, D., Smith, A.F.M., and West, M. (eds.), Bayesian Statistics 9, 393420. Oxford University Press, Oxford, UK. With Discussion.
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 51165121.
Wakefield, J. (2007). A Bayesian Measure of Probability of False Discovery in Genetic Epidemiology Studies. AJHG, 81, 208227.
See Also
ebam
, sam
, EBAMclass
, SAMclass