affymetrix snp 6

[johnsequence]

Hello,

I am running a set of affymetrix snp 6.0 chip and new in DNA stuff. Could you please recommend some softwares (e.g. R based packages)? Thanks a lot.

John

[RDW]

What's your application? For copy number analysis, the free Affymetrix Genotyping Console is pretty nice if you want a GUI tool, or try the Affymetrix Power Tools for command line versions of the algorithms. For LOH I've got better results with dChip. For an R-based framework try aroma.affymetrix. Broad's IGV is good for displaying data from multiple arrays, and their Ultrasome package does very fast copy number segmentation. Links to all these are on the aroma.affymetrix tools page:

http://aroma-project.org/node/80

I still also use an old and probably unmaintained package called CGH Explorer for looking at individual copy number profiles in detail:

http://www.ncbi.nlm.nih.gov/pubmed/15531610

[Sam64]

I use Partek genomic software but the licence is not free
Sam64