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IsoGene (version 1.0-24)

IsoGenemSAM: The five SAM test statistics calculated for both the increasing and decreasing trends

Description

The function calculates the values for the five SAM test statistics (the global likelihood test, Williams, Marcus, M, and the modified M) for the most likely direction.

Usage

IsoGenemSAM(x, y, fudge.factor)

Arguments

x
indicates the dose levels
y
gene expression for all genes
fudge.factor
the fudge factor values to be used in the SAM test statistics

Value

A list with components
E2
the SAM test statistic of global likelihood test for the likely direction of each gene.
Williams
the test statistic of Williams for the likely direction of each gene.
Marcus
the test statistic of Marcus for the likely direction of each gene.
M
the M test statistic for the likely direction of each gene.
ModM
the test statistic of the modified M for the likely direction of each gene.
direction
the direction with the higher likelihood of increasing (indicated by "u") or decreasing (indicated by "d") trend.

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.

Testing for Trend in Dose-Response Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and Resampling-Based Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.

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

isoreg, IsoGene1, Isofudge