gcrma

0th

Percentile

Robust Multi-Array expression measure using sequence information

This function converts an AffyBatch into an ExpressionSet using the robust multi-array average (RMA) expression measure with help of probe sequence.

Keywords
manip
Usage
gcrma(object,affinity.info=NULL, affinity.source=c("reference","local"),NCprobe=NULL, type=c("fullmodel","affinities","mm","constant"), k=6*fast+0.5*(1-fast),stretch=1.15*fast+1*(1-fast),correction=1, GSB.adjust=TRUE, rho=.7,optical.correct=TRUE,verbose=TRUE,fast=TRUE, subset=NULL,normalize=TRUE,...)
Arguments
object
an AffyBatch
affinity.info
NULL or an AffyBatch containing the affinities in the exprs slot. This object can be created using the function compute.affinities.
affinity.source
reference: use the package internal Non-specific binding data or local: use the experimental data in object. If local is chosen, either MM probes or a user-defined list of probes (see NCprobes) are used to estimate affinities.
NCprobe
Index of negative control probes. When set as NULL,the MM probes will be used. These probes are used to estimate parameters of non-specific binding on each array. These will be also used to estimate probe affinity profiles when affinity.info is not provided.
type
"fullmodel" for sequence and MM model. "affinities" for sequence information only. "mm" for using MM without sequence information.
k
A tuning factor.
stretch
.
correction
.
GSB.adjust
Logical value. If TRUE, probe effects in specific binding will be adjusted.
rho
correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7
optical.correct
Logical value. If TRUE, optical background correction is performed.
verbose
Logical value. If TRUE messages about the progress of the function is printed.
fast
Logical value. If TRUE a faster ad hoc algorithm is used.
subset
a character vector with the the names of the probesets to be used in expression calculation.
normalize
logical value. If 'TRUE' normalize data using quantile normalization.
...
further arguments to be passed (not currently implemented - stub for future use).
Details

Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

The tuning factor k will have different meanings if one uses the fast (add-hoc) algorithm or the empirical Bayes approach. See Wu et al. (2003)

Value

An ExpressionSet.

Aliases
  • gcrma
  • gcrma.bg.transformation.fast
  • gcrma.bg.transformation
  • GSB.adj
Examples
if(require(affydata) & require(hgu95av2probe) & require(hgu95av2cdf)){
     data(Dilution)
     ai <- compute.affinities(cdfName(Dilution))
     Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities")
}
Documentation reproduced from package gcrma, version 2.44.0, License: LGPL

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