
Thank you for quick reply. That is exactly what is required in analysis 
(i.e. confidence score and information on SNP type).

I want my output to look like this for each sample:

SNP Name    Sample ID    Allele1 - Top    Allele2 - Top    Allele1 - 
Forward    Allele2 - Forward    Chr    Position    SNP    GC Score
rs1000113    5109232032_R05C01    G    G    C    C    5    150220268    
[T/C]    0.87
rs10008492    5109232032_R05C01    A    G    T    C    4    38442114    
[T/C]    0.36
rs10008493    5109232032_R05C01    A    G    T    C    4    65127855    
[T/C]    0.91
rs10008494    5109232032_R05C01    A    T    T    A    4    19118424    
[T/A]    0.74
rs1001179    5109232032_R05C01    G    G    G    G    11    34416806    
[T/C]    0.96

This output is same as given by illumina software.
I am looking for similar kind off information for SNP . How should I 
proceed further?
Is it like annotating SNPs?

Regards,
Chintan Vora
Sr. Research Associate
Xcelris Labs Ltd.
Old Premchandnagar Road,
Bodakdev, Ahmedabad-380 054 India.
Tel: +91-79-66197777/66311114
Fax: +91-79-66309341
Email: chintan.vora@xcelrislabs.com
Website: www.xcelrisgenomics.com


On 11/29/2011 07:36 PM, Benilton Carvalho wrote:
> Say that your SnpSet object is called 'crlmmOutput', you can run:
>
> theCalls = calls(crlmmOutput)
> theConfs = confs(crlmmOutput)
>
> to get the genotype calls (1 - AA; 2 - AB; 3 - BB) and their
> respective confidence scores.
>
> b
>
> On 28 November 2011 09:32, Chintan Vora - Xcelris
> <chintan.vora@xcelrislabs.com>  wrote:
>> Dear Mathew,
>>
>> I am new to genotyping data analysis using R.
>> I was going through your package CRLMM. I used the commands
>> "readIdatFiles" and "crlmmIllumina".
>>
>> I am now wondering what to do with SNPSet object.
>>
>> Can you please explain me how can I use this object further?
>> --
>>
>> Regards,
>> Chintan Vora
>> Sr. Research Associate
>> Xcelris Labs Ltd.
>> Old Premchandnagar Road,
>> Bodakdev, Ahmedabad-380 054 India.
>> Tel: +91-79-66197777/66311114
>> Fax: +91-79-66309341
>> Email: chintan.vora@xcelrislabs.com
>> Website: www.xcelrisgenomics.com
>>
>>
>>
>> "Please don't print this e-mail unless you really need to. Save Paper, Save Trees"
>>
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