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affyPLM (version 1.48.0)

Methods for fitting probe-level models

Description

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

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Version

Version

1.48.0

License

GPL (>= 2)

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Maintainer

B M Bolstad

Last Published

February 15th, 2017

Functions in affyPLM (1.48.0)

preprocess

Background correct and Normalize
PLMset-class

Class PLMset
fitPLM

Fit a Probe Level Model to Affymetrix Genechip Data.
PLMset2exprSet

Convert a PLMset to an ExpressionSet
threestep

Three Step expression measures
ReadRMAExpress

Read RMAExpress computed expression values
normalize.ExpressionSet

Normalization applied to ExpressionSets
pseudo.coloring

Coloring pseudo chip images
threestepPLM

Three Step expression measures returned as a PLMset
internal functions

Internal affyPLM functions
MAplot

Relative M vs. A plots
bg.correct.LESN

LESN - Low End Signal is Noise Background corrections
normalize.quantiles.probeset

Quantile Normalization applied to probesets
rmaPLM

Fit a RMA to Affymetrix Genechip Data as a PLMset
normalize.scaling

Scaling normalization