[BioC] SNP Analysis

Benilton Carvalho bcarvalh at jhsph.edu
Fri Oct 23 07:06:15 CEST 2009 

The following may also be of interest:

http://www.bepress.com/jhubiostat/paper180/

b

On Oct 22, 2009, at 12:19 PM, Vincent Carey wrote:

> For a comparison of crlmm (Bioconductor) and birdseed, see
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643934/
>
> There are various interfaces between plink and R.  snpMatrix and
> SNPchip in Bioconductor should also be considered as one thinks about
> workflows for snp arrays.
>
> On Thu, Oct 22, 2009 at 8:51 AM, Peter Ganske <peterganske at mac.com>  
> wrote:
>> 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 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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