Urgent Assistance Needed for Discrepancies in GAPIT Model Results

[VidhiPriyanka13]

Dear GAPIT Forum Team,

I hope this message finds you well. I am reaching out because I have encountered an issue with my analysis using GAPIT. Despite my previous emails and sharing my file, I have not received a response. The matter is urgent, and I am seeking your immediate assistance.

Specifically, I am experiencing discrepancies in results when using different models on the same dataset. This inconsistency has persisted for the last couple of months, and I have been unable to resolve it on my own.

Could we possibly arrange a virtual call to discuss and troubleshoot the issue? Your expertise and guidance would be invaluable in helping me move forward with my research.

Thank you very much for your attention to this matter. I look forward to your prompt response.

Best regards,
Priyanka Gupta

[jiabowang]

Hi @VidhiPriyanka13 ，
Could you share details and results of Manhatton plots?

[VidhiPriyanka13]

Hi would it be possible to have virtual call please?

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________________________________ From: Jiabo Wang ***@***.***> Sent: Friday, July 19, 2024 7:52 AM To: jiabowang/GAPIT ***@***.***> Cc: Priyanka Gupta ***@***.***>; Mention ***@***.***> Subject: Re: [jiabowang/GAPIT] Urgent Assistance Needed for Discrepancies in GAPIT Model Results (Issue #133) Hi @VidhiPriyanka13<https://github.com/VidhiPriyanka13> ， Could you share details and results of Manhatton plots? — Reply to this email directly, view it on GitHub<#133 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BIACSK5RYCFBGDJ63X6XH23ZND4WBAVCNFSM6AAAAABKTAVUY6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZYHE3TOMRZGY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Pasham16]

Hi priyanka,
Did you try model selection?

[VidhiPriyanka13]

Yes I run all the model clmm mlmm farm pi and blink Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Pasham16 ***@***.***> Sent: Tuesday, September 17, 2024 4:46:50 PM To: jiabowang/GAPIT ***@***.***> Cc: Priyanka Gupta ***@***.***>; Mention ***@***.***> Subject: Re: [jiabowang/GAPIT] Urgent Assistance Needed for Discrepancies in GAPIT Model Results (Issue #133) Hi priyanka, Did you try model selection? — Reply to this email directly, view it on GitHub<#133 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BIACSK6EESVAILIF7ZJKBF3ZXAFSFAVCNFSM6AAAAABKTAVUY6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJVGM4DONJQGQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Pasham16]

what exactly are the discrepancies in the results?

[VidhiPriyanka13]

There is a mismatch in significant signal for the same dataset using different models. I believe it is supposed to be the same. Since I am travelling I will email you in details next month all the results and problems generated by GAPIT. Thank you for the follow up. Merci P

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________________________________ From: Pasham16 ***@***.***> Sent: Tuesday, September 17, 2024 11:06 AM To: jiabowang/GAPIT ***@***.***> Cc: Priyanka Gupta ***@***.***>; Mention ***@***.***> Subject: Re: [jiabowang/GAPIT] Urgent Assistance Needed for Discrepancies in GAPIT Model Results (Issue #133) what exactly are the discrepancies in the results? — Reply to this email directly, view it on GitHub<#133 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BIACSK3PUT2ORDOX5FJFBW3ZXBANXAVCNFSM6AAAAABKTAVUY6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJWGE3DGMBVGE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[VidhiPriyanka13]

All models are giving different results with same dataset. Sometimes predictive threshold and threshold line are different- Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: Pasham16 ***@***.***> Sent: Tuesday, September 17, 2024 8:36:03 PM To: jiabowang/GAPIT ***@***.***> Cc: Priyanka Gupta ***@***.***>; Mention ***@***.***> Subject: Re: [jiabowang/GAPIT] Urgent Assistance Needed for Discrepancies in GAPIT Model Results (Issue #133) what exactly are the discrepancies in the results? — Reply to this email directly, view it on GitHub<#133 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BIACSK3PUT2ORDOX5FJFBW3ZXBANXAVCNFSM6AAAAABKTAVUY6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJWGE3DGMBVGE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Pasham16]

Well, it is normal to have different significant signals in different models. But I would like to know how different they are. Please share the results when it suits you.

[VidhiPriyanka13]

[like] Priyanka Gupta reacted to your message:

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________________________________ From: Pasham16 ***@***.***> Sent: Wednesday, September 18, 2024 11:35:51 AM To: jiabowang/GAPIT ***@***.***> Cc: Priyanka Gupta ***@***.***>; Mention ***@***.***> Subject: Re: [jiabowang/GAPIT] Urgent Assistance Needed for Discrepancies in GAPIT Model Results (Issue #133) Well, it is normal to have different significant signals in different models. But I would like to know how different they are. Please share the results when it suits you. — Reply to this email directly, view it on GitHub<#133 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BIACSK77N7KT25YKONJ7Q7DZXFQRPAVCNFSM6AAAAABKTAVUY6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJYGIZDQOJUGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>