Question: SNP array - Affy data analysis
0
gravatar for David_emir
12 weeks ago by
David_emir310
India
David_emir310 wrote:

Hi All,

I have got .dat and .cell from Affymetrix 2.0 platform. It's a Custom Array-based genotyping experiment, it is designed to perform deep replication to establish disease signals and fine mapping of GWAS loci. Now my Question is how to perform an analysis so that the highly frequent genes and their respective SNPs related to a Disease can be found. It would be really helpful if you can share the analysis steps/pipeline involved or any other tutorials in this respect.

Thanks a lot for your kind help,

Regards, dave

P.S: I have around 2000 samples (Disease and normal)

ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by David_emir310
2
gravatar for Kevin Blighe
12 weeks ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

Human Mapping 10K 2.0? - that is an old platform. The easiest way (point and click) is the Genotyping Console.

In R, you can use Aroma.

Kevin

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Kevin Blighe37k

Thanks a lot Kevin, Its of great help me me, also is it possible to come up with other genes that has secondary association to a perticular disease and also how to identify the most frequent genes associated with a disease at a very early stage with this GWAS? Thanks again for your kind help. Sincerely, Dave

ADD REPLYlink written 11 weeks ago by David_emir310
1

Just to clarify, what is 'secondary association' in your mind?

ADD REPLYlink written 11 weeks ago by Kevin Blighe37k

Thanks a lot for your kind reply! it means a lot. Here Secondary association means - genes that have the secondary association to Myocardial Infraction associated genes or in Myocardial Infraction development.

ADD REPLYlink written 11 weeks ago by David_emir310

I do not know the background to your study. MI (myocardial infarction) is one of the most well-studied ailments in humans. OMIM stores known susceptibility genes:

ADD REPLYlink written 11 weeks ago by Kevin Blighe37k
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