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SAGx (version 1.46.0)

Statistical Analysis of the GeneChip

Description

A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.

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Version

Monthly Downloads

9

Version

1.46.0

License

GPL-3

Maintainer

Per Broberg

Last Published

February 15th, 2017

Functions in SAGx (1.46.0)

Gene Set Enrichment Analysis using output from samroc

Estimate proportion unchanged genes

Rank genes with respect to multiple criteria

Produces a BASE file

Output a script file to WinMIM

Fetch data from the GATC database

Calculation of fp and fn based on a vector of p-values

Estimate proportion unchanged genes

Pooling of Adjacent Violators

Calculation of F statistic by gene given a linear model

Fitting of a linear model

Estimate of the FDR and the proportion unchanged genes

A clustering function

list.intersection.p

p-value for intersection of two gene lists.

Create the union of two pathway lists

Calculate ROC curve based SAM statistic

First pass description of GeneChip data

Calculation of input of residuals from linear model

Compare two groups with respect to their RSD (CV)

list.experiments

Display all experiment names and id's

Trend analysis based on ranks

samroc.result-class

Class "samroc.result" for results of the function samrocN

Jonckheere-Terpstra trend test

Calculate ROC curve based SAM statistic

Clustering Figure of Merit

Clustering Goodness measured by Q2

Normalise arrays

Ouput matrix to LaTeX

Output a script file to WinMIM, linking clinical data and gene expression

Identify outliers in the multivariate distribution

GAP statistic clustering figure of merit

one.probeset.per.gene

Select the best probeset per gene