A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)

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Description

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

We recommend CRMA v2 for estimating allele-specific as well total SNP signals from Affymetrix SNP chips.

Usage

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  ## S3 method for class 'AffymetrixCelSet'
doCRMAv2(csR, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL,
  plm=c("AvgCnPlm", "RmaCnPlm"), drop=TRUE, verbose=FALSE, ...)
  ## Default S3 method:
doCRMAv2(dataSet, ..., verbose=FALSE)
  ## Default S3 method:
doASCRMAv2(...)

Arguments

csR, dataSet

An AffymetrixCelSet (or the name of an AffymetrixCelSet).

combineAlleles

A logical specifying whether allele probe pairs should be summed before modelling or not.

lengthRange

An optional numeric vector of length two passed to FragmentLengthNormalization.

arrays

A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.

plm

A character string specifying which type of probe-summarization model to used.

drop

If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.

verbose

See Verbose.

...

Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

If you wish to obtain allele-specific estimates for SNPs, which are needed to call genotypes or infer parent-specific copy numbers, then use argument combineAlleles=FALSE. Total copy number signals are still available. If you know for certain that you will not use allele-specific estimates, you will get slightly less noisy signals (very small difference) if you use combineAlleles=TRUE.

doASCRMAv2(...) is a wrapper for doCRMAv2(..., combineAlleles=FALSE).

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, P. Wirapati & T.P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 \& 6, Bioinformatics, 2009.

See Also

For CRMA v1, which is a multi-array methods that precedes CRMA v2, see doCRMAv1().

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