How to can analyze the Affymetrix CytoscanHD array data?

Question

[Richard Yang]

I have CytoscanHD array data of 20 pairs of cancer data(tumor/normal). Is there any efficient tools to analyze these data.How can I get the DNA copy number values and copy number segment. How could I calculate gene-level DNA segment score?

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

What are your data files? Do you have the intensities or only the ChAS report files.

If you have the intensities you can run a CNV caller for arrays like PennCNV. http://penncnv.openbioinformatics.org/en/latest/

After getting a list of CNVs and properly filtering them (segmental duplications are a must!), you can follow the plink rare CNV pipeline to analyze your data.

http://pngu.mgh.harvard.edu/~purcell/plink/cnv.shtml

Answer 2

[Irsan]

The easiest, most user-friendly and free solution is affymetrix power tools.

Answer 3

[Christian]

Nexus Copy Number (http://www.biodiscovery.com/software/nexus-copy-number-for-affymetrix/) is another quite powerful commercial solution for this type of data.