Question: How to get SNP 6.0 array data in R?
0
gravatar for agicict
3.4 years ago by
agicict140
Korea, Republic Of
agicict140 wrote:

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?

annotation snp R • 3.1k views
ADD COMMENTlink modified 3.4 years ago by Henrik Bengtsson60 • written 3.4 years ago by agicict140
3
gravatar for Henrik Bengtsson
3.4 years ago by
United States
Henrik Bengtsson60 wrote:

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)

ADD COMMENTlink written 3.4 years ago by Henrik Bengtsson60

Thank you for your kind explanation.

ADD REPLYlink written 3.4 years ago by agicict140
0
gravatar for Jan Oosting
3.4 years ago by
Jan Oosting870
Leiden, NL
Jan Oosting870 wrote:

You could use the crlmm Bioconductor package

ADD COMMENTlink written 3.4 years ago by Jan Oosting870
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