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Fers
Community Trekker

Re-coding genotype in JMPG yields incomplete output dataset

Hello,

 

I am trying to re-code a genotype data set (~ 40 k SNPs) from diploid format (eg A / G, G / C, etc) to numerical format (0, homo; 1, hete; 2, homo). The re-coding looks good, the issue is that my data output Is incomplete (it only contains ~ 29 k SNPs). I am not getting any error or massage indicating what happened with the rest of my markers.

 

Could you please give me any clue to solve this issue

 

I am using JMP Genomics 8.2

 

Thanks

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1 REPLY 1

Re: Re-coding genotype in JMPG yields incomplete output dataset

Hi @Fers,

 

That is currious. I just recoded 295988 SNPs from AA, AB, and BB to 0,1, and 2.  All of the SNPs are there. I am using JMP Genomics 9.0.

 

Give Support a call or email them at support@jmp.com and ask them what may be the problem.

 

Best,

 

Chris

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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