[BioC] SNP Analysis

[Claus-Jürgen Scholz]

Dear Peter,

indeed, Birdseed is a genotyping algorithm and I'd use it for genotype
calling of SNP6.0 arrays (best suited for this platform). If you have
the calls, export them into a table (export options and formats should
be described in the Genotyping Console manual) and analyze the genotype
frequency differences between responders and non-responders (valuable
free software is e.g. PLINK). However, n=100 is a pretty small sample
size for a GWAS...

Bests,
Claus-Jürgen


Peter Ganske schrieb:
> Dear Vincent,
> thanks for the fast replay. Well, i thought, that the Genotyping  
> console used the Birdseed Algorithm and this algorithm is an  
> Genotyping Algorithm.
>
> Its hard to find paper or groups, who worked with this array and for  
> me ( i work as a student for an institue) is hard to find the right  
> workflow without help (nobody worked here with SNP arrays in the past)
>
> So, i have 100 Arrays (100 CHP and  100 CEL files) of 100 patients. I  
> want to have a look at the SNPs of the patients. 50 are non-responder  
> and 50 are responder. There should be a difference between the two  
> groups. Since yet, i looked for any papers for getting an "general"  
> workflow for sorting out most of the SNPs of the patients.
>
> So you think i have to try this package and create the genotyping calls?
> Whats about this workflow? So are my following thought right:
>
> - The package check every SNP for every Chips and put the result in a  
> table
> - i can combine the result of the SNPs with a selection of gene i  
> want....
>
> My boss talked about a top-list of 50 genes... Maybe this can help me  
> out for the usage of CRLMM.. dont know
>
> Thanks a lot and sorry for the questions. First time for me to work  
> with SNP Arrays and the first time to work with Bioconductor/R
> All the best from Germany
> Peter
> Am 21.10.2009 um 16:11 schrieb Vincent Carey:
>
>   
>> Briefly, you can perform genotype calling with a confidence measure
>> using crlmm package, working from the CEL files.   The crlmm package
>> includes a vignette called crlmmDownstream.pdf that illustrates one
>> approach to GWAS analysis based on 6.0, using snpMatrix package.  To
>> use crlmm you will also need a metadata package called
>> genomewidesnp6crlmm.
>>
>> There are certainly other approaches possible.  Our workflow
>> documentation for this use case probably needs some enhancement.
>>
>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <Peter.Ganske at hki-jena.de 
>>     
>>> wrote:
>>>
>>> Hello,
>>> first time for me to work with SNP arrays. I got CEL- and CHP-files  
>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP-  
>>> Array 6.0 and the CHP- files are dealed with the Birdseed-  
>>> Algorithm (part of the Genotyp Console from Affymetrix as well).
>>> Is there anybody here, who worked with this arrays in the past? I  
>>> am looking for an (general) workflow for my study. I want to  
>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and  
>>> the question "why there are respoonder and non-responder for the  
>>> therapy"?
>>> I am looking for an workflow for the arrays. Is it better to work  
>>> with the CHP files or with the CEL- files?
>>> Would me great, if anybody can help me out.
>>> Thanks in advance
>>> Peter
>>>
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