IsoGene v1.0-24

0

Monthly downloads

0th

Percentile

Order-Restricted Inference for Microarray Experiments

Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.

Functions in IsoGene

Name Description
IsomaxT The maxT procedure for order restricted inference
Isoallfdr Obtaining the delta table in the SAM procedure
IsoGenemSAM The five SAM test statistics calculated for both the increasing and decreasing trends
IsoGenem The five test statistics calculated for both the increasing and decreasing trends
exampleData Dose-response microarray example data
dopamine Dose-response microarray example data
IsoGene1 The five test statistics calculated for both the increasing and decreasing trends
IsoBHPlot Plot of adjusted p-values using BH or BY adjustment
Isofudge Calculation of the fudge factor for the five SAM test statistics in the SAM procedure
IsoGene-package IsoGene
Isoqqstat Implementation of five SAM test statistics in the SAM procedure
IsoTestBH Test of monotonic trends using the five test statistics with BH or BY adjustment
IsopvaluePlot Plot of p-values from permutations under increasing or decreasing alternatives
IsoSAMPlot Plots produced using the SAM procedure
Isoqval Obtaining the list of significant genes using the SAM procedure
IsoTestSAM Obtaining the list of significant genes using the SAM procedure
IsoPlot IsoPlot
IsoRawp IsoRawp
No Results!

Vignettes of IsoGene

Name
IsoGene.Rnw
mybook4.cls
psfig.sty
pupdn1b.png
stat1a.png
No Results!

Last month downloads

Details

Type Package
Date 2015-07-15
License GPL-3
Repository CRAN
Repository/R-Forge/Project isogene
Repository/R-Forge/Revision 194
Repository/R-Forge/DateTimeStamp 2015-07-23 12:32:36
Date/Publication 2015-07-31 12:11:58
NeedsCompilation no
Packaged 2015-07-27 14:10:48 UTC; rforge

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/IsoGene)](http://www.rdocumentation.org/packages/IsoGene)