marray: maTwoSamples – R documentation

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maTwoSamples

Changing signs for two sample analysis

Taking target file information and flip the dye swaps experiments.

maTwoSamples(targetfile, normdata, Trt, Ctl, targetID = "TargetName", slidesID = "Slides", dyesID = "Dyes", RedID = 5, path = ".", output = TRUE)

`targetfile`	A data.frame containing target samples information.
`normdata`	A R object of class 'marrayNorm'
`Trt`	A character string representing "treatment" sample.
`Ctl`	A character string representing "controls" sample.
`targetID`	A character string representing the column name in 'targetfile' containing target samples information.
`slidesID`	A character string representing the column name in 'targetfile' containing the slide label.
`dyesID`	A character string representing the column name in 'targetfile' containing dye labeled information.
`RedID`	The character use to represent the Cy5 dye.
`path`	A character string representing the data directory. By default this is set to the current working directory (".").
`output`	Save and tab delimited file

An objects of 'marrayNorm' with the dye assignment adjusted.

Yee Hwa (Jean) Yang

Exploratory analysis for two-color spotted microarray data

v1.68.0

LGPL

Authors

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.

Initial release

2009-08-15