Question: How to can analyze the Affymetrix CytoscanHD array data?
0
gravatar for Richard Yang
2.1 years ago by
China
Richard Yang0 wrote:

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?

rna-seq snp • 690 views
ADD COMMENTlink modified 2.1 years ago by Christian2.5k • written 2.1 years ago by Richard Yang0
1
gravatar for QVINTVS_FABIVS_MAXIMVS
2.1 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.0k wrote:

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

ADD COMMENTlink written 2.1 years ago by QVINTVS_FABIVS_MAXIMVS2.0k
0
gravatar for Irsan
2.1 years ago by
Irsan6.3k
Amsterdam
Irsan6.3k wrote:
The easiest, most user-friendly and free solution is affymetrix power tools.
ADD COMMENTlink written 2.1 years ago by Irsan6.3k
0
gravatar for Christian
2.1 years ago by
Christian2.5k
Vienna
Christian2.5k wrote:
Nexus Copy Number (http://www.biodiscovery.com/software/nexus-copy-number-for-affymetrix/) is another quite powerful commercial solution for this type of data.
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Christian2.5k
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