Welcome!

[PennPRS]

Hi there.

Feel free to post suggestions,  bug reports or ask questions for PennPRS.

[Marie Vibeke Vestergaard]

Dear PennPRS, 

Thank you for a great and needed tool - I am looking forward to trying it out. 

In this process, I encountered an error not described in your FAQ: 

Error in sqrt(FunII.N.samplesize.tmp) :
  non-numeric argument to mathematical function
Calls: main ... PUMAS.II.FUN.I -> mclapply -> lapply -> FUN -> matrix
In addition: Warning message:
In min(matched_data$gwas_matched$N) :
  no non-missing arguments to min; returning Inf
Execution halted

This was reported in the Step 1: PUMAS Subsampling. 

It appears to be an issue with the sample size. However, I have manually entered the number of cases (1762) and controls (972) in the submission job. 

Hope you can help!

All the best

[Bingxin Zhao]

Dear Marie,

 

  Thank you so much for trying our tool and reporting this error!

Did you query data from the GWAS Catalog? If so, could you please share the study ID (GCST xxx) with us? Perhaps your log file as well? We will look into this soon!

Best wishes,

Bingxin

[Zhao, Bingxin]

Dear Marie,

 

  Thank you so much for trying our tool and reporting this error!

Did you query data from the GWAS Catalog? If so, could you please share the study ID (GCST xxx) with us? Perhaps your log file as well? We will look into this soon!

Best wishes,

Bingxin

---

From: 'Marie Vibeke Vestergaard' via PennPRS <pen...@googlegroups.com>
Sent: Wednesday, February 12, 2025 6:23 AM
To: PennPRS <pen...@googlegroups.com>
Subject: Re: Welcome!

 

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[Li BX]

Hello Marie,

 

Thank you for using PennPRS.

 

The error you encountered is due to inputting numerical sample sizes instead of column names. When uploading data, we do not accept a numerical value for “N.” Instead, we require the uploaded data contains sample size columns and expect the user to fill in the “NCase” and “NControl” fields with the corresponding column names. For detailed instructions on uploading data, please refer to our tutorial (link)

 

Additionally, we noticed that you selected “GCST004053” when querying data. Currently, we only support harmonized queryable data, which is displayed on the “Queryable Data” page. Please ensure that your input ID is included in our queryable data before proceeding. For further details and examples, please check the query data section of our tutorial (link)

 

Please let us know if you have more issues or questions!

 

Sincerely,

PennPRS Team

 

From: 'Marie Vibeke Vestergaard' via PennPRS <pen...@googlegroups.com>
Date: Wednesday, February 12, 2025 at 06:23
To: PennPRS <pen...@googlegroups.com>
Subject: Re: Welcome!

[Marie Vibeke Vestergaard]

Dear PennPRS Team,

 

Thank you for a swift reply! It makes sense – I will try it out.

 

Good luck with the paper submission process! I will keep an eye out, so that I can cite your paper, if I end up including the results in my project.

 

All the best,

Marie

 

 

Med venlig hilsen / Kind Regards

 

 

 

 

Marie Vibeke Vestergaard

Ph.D. studerende  /  Ph.D. Student

 

Center for Molecular Prediction of Inflammatory Bowel Disease – PREDICT

Department of Clinical Medicine  |  The Faculty of Medicine, Aalborg University

 

T:(+45) 9940 3529  |  M:(+45) 4296 3689  |  Email: mar...@dcm.aau.dk  |  Web: www.klinisk.aau.dk  |  Web: www.predictibd.dk

 

PREDICT | AAU CPH | A.C. Meyers Vænge 15, A | 2450 Copenhagen SV

The Faculty of Medicine, Aalborg University

 

T:(+45) 9940 7767 | Email: mar...@dcm.aau.dk | www.predictibd.dk | 

Twitter: @PREDICTIBD

  

PREDICT | AAU CPH | A.C. Meyers Vænge 15,A 

[Jin Jin]

Great, thanks! Please let us know if you have more questions.