Comparision of CNVs from Two different platfroms

[meher]

Hi,

I am quiet new to CNV analysis and i have a general query.

I have SNP array data from Affymetrix and Illumina, would you please comment (or provide a reference) on the pros and cons of using two different platforms, like the possible issues to make a comparision between the CNV results? possible batch effects etc..

What steps should be considered when using data from two different platforms. Any references would be helpful.

[mastal]

Do you mean that you have data from Affymetrix genotyping arrays and Illumina genotyping arrays, or Affymetrix arrays and Illumina sequencing data?

[meher]

Do you mean that you have data from Affymetrix genotyping arrays and Illumina genotyping arrays, or Affymetrix arrays and Illumina sequencing data?

Yes, the data is from Genotyping arrays i.e. Affymetrix genotyping arrays and Illumina genotyping arrays.

[dickie_ho]

Hey Meher
Pros i would say having more data, cons - different methods to get your data into penncnv (or your downstream pipeline).
It really depends on what type of analysis you want to do downstream ?? Association ?? or looking at specific CNVs ?? Batch affects I would assume depending on you preferences (i normally go at least 10 probes and at least 20kb in size -- only because i have sequencing data as well as the arrays) ... if u have access to the DNA, run a taqman on specific CNVs detected on both platforms........ but from my experience, because of the size of CNVs you shouldn't have as many issues as SNPs ... another thing you might like to do is compare all the probes between the two different types of arrays and exclude exclusive probes... I hope this helps and not a repeat of what you already know

cheers
Josh