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ulipkin
Level I

JMP Genomics r2 >1.0

How can it be, that I am getting CorrCoeff2 values above 1.0, up to 2.0?

12 REPLIES 12
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statman
Level VII

Re: JMP Genomics r2 >1.0

Can't tell from what you posted.  Could you provide some info?  What version of JMP, which OS, and perhaps screen shots or the journal of the analysis you performed.

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ulipkin
Level I

Re: JMP Genomics r2 >1.0

Thanks for the reply,

Attached is an Excel file telling the story. I am using JMP Genomics whose
data are presented in the first worksheet 'JMP'. I submitted the genotypes
presented in the worksheet 'Genotypes' to the LD analysis (worksheet 'JMP
Linkage Disequilibrium'), and got the LD r2 matrix presented in the last
worksheet. Values above 1.0 are labeled. By definition, r2 cannot have a
value above 1.0. I am using JMP Genomics for some years, many LD analyses,
and I never saw something like this. What is going on?

Thanks,

Ehud Lipkin


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Thierry_S
Level VI

Re: JMP Genomics r2 >1.0

Hi,
I think you forgot to include the file(s) you referred to in your last message or there might be a problem with the JMP forum attachment module.
Best,
TS
Thierry R. Sornasse
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ulipkin
Level I

Re: JMP Genomics r2 >1.0

Hello TS,

It was attached, and attached again. If you didn't get it again, please let
me what to do.

All the best,

Ehud Lipkin


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Thierry_S
Level VI

Re: JMP Genomics r2 >1.0

Hi Ehud,

 

I wonder if your Excel file is larger than 95 Mb which is the maximum attachment size allowed on the JMP Forum.

Otherwise, If you use the "Reply" (not "Quick Reply"), you should see the following display at the bottom of the page:

Annotation 2020-10-04 131000.png

 

But I assume that is what you did in your prior attempts so there might be something wrong with your file and/or the JMP Forum.

Best,

TS

 

Thierry R. Sornasse
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ulipkin
Level I

Re: JMP Genomics r2 >1.0

The file is 247 KB. So what to do? Maybe you can give me a regular email
address, just to transfer the file. Then we can continue here.




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Thierry_S
Level VI

Re: JMP Genomics r2 >1.0

Sorry, I cannot do that.
Best,
TS
Thierry R. Sornasse
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Re: JMP Genomics r2 >1.0

Hi @ulipkin,

Can you tell us which version of JMP Genomics you are using? Look under Help>About JMP

Also, try uploading the file as a .csv

Thanks,

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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Re: JMP Genomics r2 >1.0

Also, it would help if you could let us know the options you have selected in each of the tabs of the Linkage Disequilibrium dialog.
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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