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GeneNetwork (2nd generation)
http://gn2.genenetwork.org/
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[Bug] Phenotype record info becomes NA when added to collection #447

Closed emilyjyao closed 4 years ago

emilyjyao commented 4 years ago

Describe the bug When I search within the BXD Published Phenotypes dataset, everything works correctly and all of the records have all the column information correctly filled out. However, when I try to add these phenotype records to a collection, the location information disappears and many rows have N/A in the Additive Effect column. (see below for screenshots). Thus I am not able to generate a correlation matrix because it gives me an error saying "GeneNetwork error: Array must not contain infs or NaNs".

To Reproduce

Expected behavior The phenotype records should appear within the collection with all of the correct information.

Screenshots

Below is a screenshot of my search results - as you can see, all the information is complete. image

When I try to add these results to my collection, the location disappears and many Additive Effect cells become N/A. image

Environment setup:

robwwilliams commented 4 years ago

Thanks Emily. We will fix.

On Tue, Sep 29, 2020 at 2:06 PM emilyjyao notifications@github.com wrote:

Describe the bug When I search within the BXD Published Phenotypes dataset, everything works correctly and all of the records have all the column information correctly filled out. However, when I try to add these phenotype records to a collection, the location information disappears and many rows have N/A in the Additive Effect column. (see below for screenshots). Thus I am not able to generate a correlation matrix because it gives me an error saying "GeneNetwork error: Array must not contain infs or NaNs".

To Reproduce

  • Search within the BXD published phenotypes dataset
  • Add the record rows to a collection

Expected behavior The phenotype records should appear within the collection with all of the correct information.

Screenshots

Below is a screenshot of my search results - as you can see, all the information is complete. [image: image] https://user-images.githubusercontent.com/72101759/94603285-09d6f680-0264-11eb-9d86-18b8812cfde7.png

When I try to add these results to my collection, the location disappears and many Additive Effect cells become N/A. [image: image] https://user-images.githubusercontent.com/72101759/94603393-2ffc9680-0264-11eb-904a-7ff2aacf7bd0.png

Environment setup:

  • OS: Windows

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-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center 71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405 Tele/Cell: 901 604 4752 EMAIL: rwilliams@uthsc.edu or labwilliams@gmail.com

zsloan commented 4 years ago

Thanks for pointing this out - the issue ended up being that the template checks if casting the additive effect to a float returns "> 0" (which excluded all additive effects below 0). Apparently it's supposed to just be "!= 0" (where the template language returns 0 if it can't be cast to a float).

I'll go ahead and make the fix today, but in the meanwhile it's probably worth mentioning that there's no actual difference in the underlying data; the web page is just wrongly displaying "N/A."

On Tue, Sep 29, 2020 at 2:16 PM robwwilliams notifications@github.com wrote:

Thanks Emily. We will fix.

On Tue, Sep 29, 2020 at 2:06 PM emilyjyao notifications@github.com wrote:

Describe the bug When I search within the BXD Published Phenotypes dataset, everything works correctly and all of the records have all the column information correctly filled out. However, when I try to add these phenotype records to a collection, the location information disappears and many rows have N/A in the Additive Effect column. (see below for screenshots). Thus I am not able to generate a correlation matrix because it gives me an error saying "GeneNetwork error: Array must not contain infs or NaNs".

To Reproduce

  • Search within the BXD published phenotypes dataset
  • Add the record rows to a collection

Expected behavior The phenotype records should appear within the collection with all of the correct information.

Screenshots

Below is a screenshot of my search results - as you can see, all the information is complete. [image: image] < https://user-images.githubusercontent.com/72101759/94603285-09d6f680-0264-11eb-9d86-18b8812cfde7.png

When I try to add these results to my collection, the location disappears and many Additive Effect cells become N/A. [image: image] < https://user-images.githubusercontent.com/72101759/94603393-2ffc9680-0264-11eb-904a-7ff2aacf7bd0.png

Environment setup:

  • OS: Windows

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/447, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AC55V7GLV3DVL6R3P5DFOYTSIIV2NANCNFSM4R6FW3WA

.

-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center 71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405 Tele/Cell: 901 604 4752 EMAIL: rwilliams@uthsc.edu or labwilliams@gmail.com

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/447#issuecomment-700926616, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANQJGFTJ3LH7BU4JLEC3Y3SIIW7PANCNFSM4R6FW3WA .