## Normalisation / Illumina SNP arrays

### Description

Preprocesses Illumina SNP array genotype call-files and/or calls allels and their corresponding confidence values from Illumina GenCall software output.

### Parameters

- Allel calling method
- cdfName
- Signal-to-noise ratio

### Details

Reformats Illumina GenCall output to Chipster format or computes the genotype values using the CRLMM method as implemented in the package crlmm. The cdfName parameter defines the CDF name to be used in the CRLMM analysis (human1mduov3b, human1mv1c, human370quadv3c, human370v1c, human550v3b, human610quadv1b, human650v3a, human660quadv1a, humanomni1quadv1b, humanomniexpress12v1b). By default, CDF names are extracted from the chips themselves for CRLMM analysis. In the case, your chip is not among the listed ones, contact support.

In the CRLMM implementation, bad-quality chips are filtered out from the data based on their signal-to-noise ratio. Lowering the cutoff can decrease the overall quality of SNP calls but will increase the amount of chips passed to further analysis.

### Output

A tab-delimited text file containing gene names and expression estimates. This file is suitable for all further analyses.

### References

This tool uses Bioconductor package oligo. You can cite the package as:

Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high density oligonucleotide snp array data. Biostatistics, Dec 2006.

Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics. 2010, 26:242-9.

Ritchie ME, Carvalho BS, Hetrick KN, TavarŽ S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009, 25:2621-3.