Benilton,

justCRLMM works fine now in our framework, with a batch_size  
parameter equals to 5000.
But, does a relatively low value for this parameter influence the  
reliability of the results?
Best regards. Olivier

--  
____________________________________

Olivier G. Nuñez
Email: onunez@iberstat.es
Tel : +34 663 03 69 09
Web: http.//www.iberstat.es

____________________________________



El 05/04/2008, a las 23:47, Benilton Carvalho escribió:

> Hi Olivier,
>
> there's no "by chromosome" option with justCRLMM...
>
> On the other hand, there is a "batch_size" argument, whose default  
> value is 40000. That means that 40K SNPs will be processed at a  
> time. Decreasing it might be helpful in your scenario.
>
> Let me know how it goes,
>
> b
>
> On Apr 5, 2008, at 1:46 PM, Olivier Nuñez wrote:
>> Dear Bemilton,
>>
>> we are trying to obtain the Genotype calls using justCRLMM for a  
>> sample of 50 cases (500K SNP chips).
>> Despite our 3Gb of RAM, the usual "cannot allocate vector of  
>> size ..." error occurs systematically.
>> So we think to apply justCRLMM chromosome by chromosome on the  
>> whole sample in order to not exceed the memory limitations to a  
>> single process.
>> Is this method compatible with CRLMM? If yes, what is the best way  
>> to proceed under oligo.
>> Thanks for your help.
>> Best regards. Olivier
>>
>>
>> -- ____________________________________
>>
>> Olivier G. Nuñez
>> Email: onunez@iberstat.es
>> Tel : +34 663 03 69 09
>> Web: http.//www.iberstat.es
>>
>> ____________________________________
>>
>>
>>
>


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