Description Usage Arguments Value Note Author(s) References See Also Examples
The function obtains the list of significant genes using the SAM procedure for the five test statistics (the global likelihood test, Williams, Marcus, M, and the modified M).
1 | IsoTestSAM(x, y, fudge, niter, FDR, stat)
|
x |
numeric vector containing the dose levels |
y |
data frame of the gene expression with Probe ID as row names |
fudge |
option used for calculating the fudge factor in the SAM test
statistic, either |
niter |
number of permutations to use |
FDR |
choose the desired FDR to control |
stat |
choose one of the five test statistics to use |
A list with components
sign.genes1 |
a list of genes declared significant using the SAM procedure in a matrix of 5 columns. The first colomn is the probe id, the second column is the corresponding row number of the probe in the dataset, and the third column is the ordered test statistic values, and the fourth column is the q-values of the SAM procedure. The last two columns are raw p-values based on permutations and BH adjusted p-values. |
qqstat |
output of Isoqqstat |
allfdr |
output of Isoallfdr |
This function obtains the list of significant genes using 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.
Lin et al.
Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors). (2012) Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R. 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.
isoreg
, Isofudge
, IsoGenemSAM
, Isoqqstat
,
Isoallfdr
,Isoqval
, IsoSAMPlot
1 2 3 4 5 6 7 8 | 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
SAM.obj <- IsoTestSAM(x, y, fudge="pooled", niter=50, FDR=0.05, stat="E2")
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