Isoallfdr
From IsoGene v1.0-24
by Rudradev Sengupta
Obtaining the delta table in the SAM procedure
The function obtains the delta table in the SAM procedure for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).
- Keywords
- htest
Usage
Isoallfdr(qqstat, ddelta, stat)
Arguments
- qqstat
- output from function Isoqqstat containing the test statistics of permutations
- ddelta
- give a list of values as cut-off to find the number of significant genes in the SAM procedure. If unspecified, the default value is assigned using the centiles of the absolute difference between the observed and expected test statistics.
- stat
- choose one of the five test statistics to use
Value
-
dtable: the delta table in the SAM procedure containing
six columns. The first column is the cut-off value to find
the number of significant genes, the second column is the
meidan number of false positives, the third column is the 90%
percentile number of false positives, the fourth column is
the number of significant genes, the fifth column is the median
FDR, and the last column is the 90% FDR.
Note
This function calculates the delta table in the SAM procedure for the five test statistics. To use the SAM procedure, the number of genes in the dataset is preferably larger than 500.
References
Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R, Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors), (2012), Springer.
IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2(1).
See Also
Examples
set.seed(1234)
x <- c(rep(1,3),rep(2,3),rep(3,3))
y1 <- matrix(rnorm(4500, 1,1),500,9) ## 500 genes with no trends
y2 <- matrix(c(rnorm(1500, 1,1),rnorm(1500,2,1),
rnorm(1500,3,1)),500,9) ## 500 genes with increasing trends
y <- data.frame(rbind(y1, y2)) ##y needs to be a data frame
qqstat <- Isoqqstat(x, y, fudge="pooled",niter=50)
allfdr <- Isoallfdr(qqstat,,stat="E2")
Community examples
Looks like there are no examples yet.