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jiabowang / GAPIT

Genome Association Predict Integrate Tools
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Discrepancies in GWAS Results with Updated Version #120

Open VidhiPriyanka13 opened 5 months ago

VidhiPriyanka13 commented 5 months ago

Hello GAPIT Forum,

After updating to the latest version, I'm getting different GWAS results from the same data file. Also, there are discrepancies between analyses run on different machines. Any insights on the necessary steps for the updated version and why results differ would be appreciated.

Thank you P

yuru0503 commented 4 months ago

I also found out it had different results between GAPIT3.4 and GAPIT3.3. Based on my understanding of my GWAS research, I think that the outputs from the GAPIT3.3 version are the correct ones.

Hadi-Hoda-AghBaba commented 4 months ago

Hi there, are you using the same model?

VidhiPriyanka13 commented 4 months ago

Yes same model

Get Outlook for iOShttps://aka.ms/o0ukef

From: Hadi-Hoda-Aghbaba @.> Sent: Sunday, April 28, 2024 7:04:32 PM To: jiabowang/GAPIT @.> Cc: Priyanka Gupta @.>; Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

Hi there, are you using the same model?

— Reply to this email directly, view it on GitHubhttps://github.com/jiabowang/GAPIT/issues/120#issuecomment-2081689537, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BIACSKZNF6HWFIJCKBAY5WLY7V6ABAVCNFSM6AAAAABGS2Z566VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBRGY4DSNJTG4. You are receiving this because you authored the thread.Message ID: @.***>

Hadi-Hoda-AghBaba commented 4 months ago

Could you please send both codes here. Cheers

Hadi-Hoda-AghBaba commented 4 months ago

Also the Manhattan plots as well. tnx

VidhiPriyanka13 commented 4 months ago

Same Script in my server i used as follows

myY <- read.table("/home/prgup1/icsw/fast-gbs_v2/results/gwas/TKW1.txt", head = TRUE) myG <- read.table("/home/prgup1/icsw/fast-gbs_v2/results/gwas/Genotyping_file_21Chr_153K_withS_withoutsemicoloumn2_142G.hmp.txt", head = FALSE) myGAPIT <- GAPIT(Y=myY,G=myG,PCA.total=3, model=c("FarmCPU"), Multiple_analysis=TRUE, Model.selection = TRUE)[https://res-h3.public.cdn.office.net/assets/mail/file-icon/png/zip_16x16.png]wheat-trial.ziphttps://ulavaldti-my.sharepoint.com/:u:/g/personal/prgup1_ulaval_ca/EetikM47OVhIm_EQ11siwlkB1iznkTz_mP-g5QHs7n6i8g

[cid:fc22e810-fdc1-4c4c-b817-0c1deb1bed27] [cid:247a11dd-ad10-42fa-859f-10168d34ad53]

From: Hadi-Hoda-AghBaba @.> Sent: Sunday, April 28, 2024 11:12 PM To: jiabowang/GAPIT @.> Cc: Priyanka Gupta @.>; Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

Also the Manhattan plots as well. tnx

— Reply to this email directly, view it on GitHubhttps://github.com/jiabowang/GAPIT/issues/120#issuecomment-2081819802, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BIACSKYVTUNDMSKRIDNCSPTY7W3BJAVCNFSM6AAAAABGS2Z566VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBRHAYTSOBQGI. You are receiving this because you authored the thread.Message ID: @.***>

Hadi-Hoda-AghBaba commented 4 months ago

Hi,

this link doesn;t work. Pls send a screen shot of your Manhattan plots.

Try this code to see if it solves the problem:

myGAPIT <- GAPIT (Y=myY, G=myG, NJtree.group=5, NJtree.type=c("fan"), kinship.algorithm = "VanRaden", model=c("FarmCPU"), Multiple_analysis=TRUE, Model.selection = TRUE)

VidhiPriyanka13 commented 4 months ago

Hi can I share with you the complete dataset- so that you can check and i will also share the error I am receiving? Is there any possibility to have a virtual call with you please

From: Hadi-Hoda-AghBaba @.> Sent: Tuesday, April 30, 2024 3:07 AM To: jiabowang/GAPIT @.> Cc: Priyanka Gupta @.>; Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

Hi,

this link doesn;t work. Pls send a screen shot of your Manhattan plots.

Try this code to see if it solves the problem:

myGAPIT <- GAPIT (Y=myY, G=myG, NJtree.group=5, NJtree.type=c("fan"), kinship.algorithm = "VanRaden", model=c("FarmCPU"), Multiple_analysis=TRUE, Model.selection = TRUE)

— Reply to this email directly, view it on GitHubhttps://github.com/jiabowang/GAPIT/issues/120#issuecomment-2084533074, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BIACSK3RA6J6GU53LCXK3X3Y747L3AVCNFSM6AAAAABGS2Z566VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGUZTGMBXGQ. You are receiving this because you authored the thread.Message ID: @.***>

Hadi-Hoda-AghBaba commented 4 months ago

Hi there, yes good idea. Send me through the data. Let's look at the data and we'll go from there :) Cheers

jiabowang commented 4 months ago

Recently, we are revising some functions. So that makes a mistake. Now, through comparison results and revision, the results should be correct.

Lightoscope commented 4 months ago

I don't know if it's related, but I'm getting different results when GAPIT calculates kinship and when that output file, 'GAPIT.Genotype.Kin_Zhang.csv' in this case, is used as KI in an otherwise identical run.

VidhiPriyanka13 commented 2 months ago

Dear GAPIT forum,

I need your help troubleshooting an issue I'm facing with GWAS analysis using different models. FarmCPU, Blink, and MLMM are providing different results for the same traits. If you agree, I can share my genotyping and phenotyping files with you for further analysis.

Thank you for your assistance.

Best regards,

P

From: Ryan Disney @.> Sent: Sunday, May 19, 2024 8:13 PM To: jiabowang/GAPIT @.> Cc: Priyanka Gupta @.>; Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

I don't know if it's related, but I'm getting different results when GAPIT calculates kinship and when that output file, 'GAPIT.Genotype.Kin_Zhang.csv' in this case, is used as KI in an otherwise identical run.

— Reply to this email directly, view it on GitHubhttps://github.com/jiabowang/GAPIT/issues/120#issuecomment-2119466630, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BIACSK2IHD5IK23Q45E2LXTZDE5Z7AVCNFSM6AAAAABGS2Z566VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJZGQ3DMNRTGA. You are receiving this because you authored the thread.Message ID: @.***>

VidhiPriyanka13 commented 2 months ago

[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/txt_16x16.png]genotying_fileHeteroMissing_80K_SNPs_corrected_NN.hmp.txthttps://ulavaldti-my.sharepoint.com/:t:/g/personal/prgup1_ulaval_ca/EdbqN1dgKVRAop9PBkz0Q8EB-P1NRMfr-QXLkjfaeBNRjw

Here is my file. Would it be possible to have a virtual call to fix the issue? I have been struggling with it for the last couple of months. Please somebody in your team can assist me.

Thanks,

P

From: Priyanka Gupta @.> Sent: Wednesday, July 3, 2024 11:39 AM To: jiabowang/GAPIT @.>; jiabowang/GAPIT @.> Cc: Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

Dear GAPIT forum,

I need your help troubleshooting an issue I'm facing with GWAS analysis using different models. FarmCPU, Blink, and MLMM are providing different results for the same traits. If you agree, I can share my genotyping and phenotyping files with you for further analysis.

Thank you for your assistance.

Best regards,

P

From: Ryan Disney @.> Sent: Sunday, May 19, 2024 8:13 PM To: jiabowang/GAPIT @.> Cc: Priyanka Gupta @.>; Author @.> Subject: Re: [jiabowang/GAPIT] Discrepancies in GWAS Results with Updated Version (Issue #120)

I don't know if it's related, but I'm getting different results when GAPIT calculates kinship and when that output file, 'GAPIT.Genotype.Kin_Zhang.csv' in this case, is used as KI in an otherwise identical run.

— Reply to this email directly, view it on GitHubhttps://github.com/jiabowang/GAPIT/issues/120#issuecomment-2119466630, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BIACSK2IHD5IK23Q45E2LXTZDE5Z7AVCNFSM6AAAAABGS2Z566VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJZGQ3DMNRTGA. You are receiving this because you authored the thread.Message ID: @.***>

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