[BioC] SNP Analysis

[Scholz Claus-Jürgen]

Dear Peter,

PLINK is simply a convenient implementation of analysis tasks usually
performed in association studies. If that's not enough, further
processing of PLINK output is easily done with R - it's designed for
that purpose. PLINK is actually standard software, it's freely available
and also well documented on the website
(http://pngu.mgh.harvard.edu/~purcell/plink/) therefore it might be
worth having at look at it. If you prefer R/Bioconductor, there are the
Packages GeneticsBase, SimHap (my personal favourite), GenABEL,
SNPassoc...

Bests,
Claus-Jürgen


>>> Peter Ganske <peterganske at mac.com>  >>>
Dear Claus- Jürgen,
thanks for the reply. In which way you would analyze the genotype  
frequency wit PLINK?
And why you use this program instead of any bioconductor- package?
All the best and thanks in advance
Peter



Am 22.10.2009 um 13:13 schrieb 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 w
ith regard to SNPs and
>>>> the question "why there are respo>>>> 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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