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jiabowang / GAPIT

Genome Association Predict Integrate Tools
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Many False-Positives #115

Open Sanewsg opened 5 months ago

Sanewsg commented 5 months ago

All GWAS models in GAPIT appear to be giving very different results from previous analysis of the same files just a few weeks ago. In each case, there are many SNPs, possibly hundreds above the P<0.05 cutoff on each chromosome. QQ plots are irregular and non-sensical. The models run without any error messages even though the results are obviously erroneous with hundreds of false-positives. Analysis of the same files in Tassel gives results as expected. It is not related to imputation. Has anyone else had this experience?

jiabowang commented 5 months ago

Hi,

Could you send the Manhattan plots and QQ plots here? Recently, we did not change code in the GAPIT GWAS function.

Sanewsg commented 5 months ago

Hi Jiabo Please see attached plots and code. Previously, these files indicated no significant loci using Blink but 2 using FarmCPU.

myGAPIT <- GAPIT(G=myG, output.numerical=TRUE) myGD=myGAPIT$GD myGM=myGAPIT$GM

myGAPIT<-GAPIT(

G=myG,

Y=myY[,c(1,2)], GD=myGD, GM=myGM, PCA.total=2,

Model.selection = TRUE,

Random.model = F, kinship.algorithm = ("Van Raden"), Multiple_analysis = FALSE, file.output = T, model=c("BLINK"), cutOff=0.05 ) Many thanks Garth

From: Jiabo Wang @.***> Sent: Sunday, April 7, 2024 12:07 PM To: jiabowang/GAPIT Cc: Garth Sanewski; Author Subject: Re: [jiabowang/GAPIT] Many False-Positives (Issue #115)

Hi, Could you send the Manhattan plots and QQ plots here? Recently, we did not change code in the GAPIT GWAS function. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the

Hi,

Could you send the Manhattan plots and QQ plots here? Recently, we did not change code in the GAPIT GWAS function.

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jiabowang commented 5 months ago

I can not see the figures. Please send them to my email: wangjiaboyifeng@163.com Thanks.