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@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
>>
>>
>> The information contained in this email and any attachments is  
>> confidential and may be subject to copyright or other intellectual  
>> property protection. If you are not the intended recipient, you are  
>> not authorized to use or disclose this information, and we request  
>> that you notify us by reply mail or telephone and delete the  
>> original message from your mail system.
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> The information contained in this email and any attachments is  
> confidential and may be subject to copyright or other intellectual  
> property protection. If you are not the intended recipient, you are  
> not authorized to use or disclose this information, and we request  
> that you notify us by reply mail or telephone and delete the  
> original message from your mail system.
>
> The information contained in this email and any attachments is  
> confidential and may be subject to copyright or other intellectual  
> property protection. If you are not the intended recipient, you are  
> not authorized to use or disclose this information, and we request  
> that you notify us by reply mail or telephone and delete the  
> original message from your mail system.


	[[alternative HTML version deleted]]

