comparing GenABEL and PLINK

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OGV
Posts: 1
Joined: Wed Dec 10, 2014 11:20 am

comparing GenABEL and PLINK

Postby OGV » Wed Dec 10, 2014 11:54 am

Hello,

I performed an association study in GenABEL and PLINK. Results, especially for p-values corrected by inflation factor are different.
As an example, I am using the "srdata" data.
The PLINK version is 1.07. R version is 3.0.2 (2013-09-25), GenABEL version is 1.8.0.

Code: Select all

data(srdta)
#additive model in GenABEL
mlreg.qt <- mlreg(qt1~sex, data=srdta, trait="gaussian",gtmode = "additive")
descriptives.scan(mlreg.qt, sort="Pc1df")

*export data to PLINK

Code: Select all

export.plink(data= srdta, filebasename=".../test",
             phenotypes=c("qt1","sex"))
#additive model in PLINK
./plink --bfile /.../test \
--pheno /.../test.phe \
--pheno-name qt1 \
--covar /.../test.phe \
--covar-name sex --linear  --adjust --out /.../test_adjusted --noweb


Output from GenABEL
descriptives.scan(mlreg.qt, sort="Pc1df")
Summary for top 10 results, sorted by Pc1df
Chromosome Position Strand A1 A2 N effB se_effB chi2.1df P1df Pc1df effAB effBB chi2.2df P2df
rs4803 1 1267000 + G A 2387 -0.11442639 0.02983568 14.708910 0.0001254521 0.0008781546 NA NA NA NA
rs4807 1 1267500 + A T 2380 0.10674032 0.02970848 12.909106 0.0003269875 0.0018287167 NA NA NA NA

Output from PLINK
CHR SNP UNADJ GC BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY
1 rs4803 0.0001287 0.0003706 0.1072 0.1072 0.1017 0.1017 0.1072 0.783
1 rs4807 0.0003336 0.0008505 0.2779 0.2776 0.2427 0.2424 0.1374 1

Inflation factor in GeNABEL

Code: Select all

> estlambda(mlreg.qt[,"P1df"],plot=F)
$estimate
[1] 1.32892

$se
[1] 0.002435024


Inflation factor in PLINK
Genomic inflation factor (based on median chi-squared) is 1.15714
Mean chi-squared statistic is 1.28928

The difference in results ere observed for all type of genetic models (allelic, dominant and etc.).

Could you explain the difference in results between GenABEL and PLINK?

Thank you in advance.
Last edited by lckarssen on Thu Dec 11, 2014 4:53 pm, edited 1 time in total.
Reason: Reformatted part of the input and output with the [code] tag

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