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Block: doCRMAv1() / doASCRMAv1()

Author: Henrik Bengtsson
Created on: 2010-05-17
Last updated: 2010-08-05

The CRMA, or to better distinguish it from newer versions, CRMA v1, is a preprocessing method for Affymetrix 10K-500K SNP arrays presented in Bengtsson, Irizarry, Carvalho, and Speed (2008). It was optimized to estimate high-quality total copy number (TCN) estimates from the 500K chip type. Later the CRMA v2 method (Bengtsson, Wirapati, and Speed, 2009) was designed, which is what is now recommended. However, in case CRMA v1 is wanted, we provide the doCRMAv1() and doASCRMAv1() methods.

Usage

ds <- doCRMAv1("HapMap270,testSet", chipType="Mapping250K_Nsp")
ds <- doCRMAv1("HapMap270,testSet", chipType="Mapping50K_Hind240")
ds <- doCRMAv1("GSE8605", chipType="Mapping10K_Xba142")

Argument 'verbose': Since this will take minutes or hours, we suggest that you add argument verbose=-10 to see some verbose output while processing the data set.

The CRMA v1 is by definition a multi-array method, which means that it is not possible to process a subset of the arrays in a data set without affecting the final results. This is only possible for the CRMA v2 method.

Allele-specific copy-number (ASCN) estimates: By adding argument combineAlleles=FALSE to the above, allele-specific CNs will be estimated (for SNPs). Alternatively, use doASCRMAv1(), which is short for doCRMAv1(..., combineAlleles=FALSE). The default is to estimate total CNs (combineAlleles=TRUE). The estimated total CNs will differ slightly when using the two alternatives and the CRMA v1 method has been optimized for total CNs (as in CRMA paper).

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho, et al. "Estimation and assessment of raw copy numbers at the single locus level". Eng. In: Bioinformatics (Oxford, England) 24.6 (Mar. 2008), pp. 759-67. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btn016. PMID: 18204055.

[2] H. Bengtsson, P. Wirapati, and T. P. Speed. "A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6". Eng. In: Bioinformatics (Oxford, England) 25.17 (Sep. 2009), pp. 2149-56. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btp371. PMID: 19535535.