How to get SNP 6.0 array data in R?

Question

[agicict]

Hi.

I currently downloaded a number of SNP datasets from GEO (CCLE)

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36138

Also I downloaded Genomewide affymetrix 6.0 SNP array annotation data from affymetrix site.

http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_6

I imported the SNP 6.0 CEL files using affy package's ReadAffy.

Strangely, every CEL files has approximately 7,000,000 rows but affymetrix annotation data has around 900,000 rows.

What is right way to match probes?

[Jan Oosting]

You could use the crlmm Bioconductor package

Answer 1

[Henrik Bengtsson]

The GenomeWideSNP_6 chip type has 6,892,960 probes (never changes). These probes are arranged in probe sets ("units") corresponding to 934,946 bi-allelic SNPs and 946,371 non-polymorphic single-probe CN loci. The exact number differ slightly between genome builds.

Check out the aroma.affymetrix R package, cf. http://aroma-project.org/. It has several ready pipelines for GenomeWideSNP_6, especially for copy-number analysis.

/Henrik
(author of aroma.affymetrix)

[agicict]

Thank you for your kind explanation.