Question: Eqtl Mapping Choice
gravatar for J.F.Jiang
7.7 years ago by
J.F.Jiang860 wrote:

Hi all,

I am mapping the SNP to gene expression to find the cis and trans eQTL.

First I tried the R package MatrixEQTL, however, finding too much trans-eQTLs, which make me doubt about the results. Even I appied several covariates to adjust the results, it seems the condition is not changed.

So here is the problem, which approach should I use to do the mapping, since r/qtl seems little complex to me and plink requires too much time for calculation.

Now i have the genotyping data with plink bed format, and an expression matrix for ~20k genes.

Could some one help me, and some step-by-step tutorials?


expression eqtl snp • 2.6k views
ADD COMMENTlink modified 5.7 years ago by Zhenyu Zhang270 • written 7.7 years ago by J.F.Jiang860

Dear Jiang, 

Where you able to find a solution to this... I am currently facing a similar challenge. 


B regs


ADD REPLYlink written 6.4 years ago by dharl70
gravatar for Zhenyu Zhang
5.7 years ago by
Zhenyu Zhang270
United States
Zhenyu Zhang270 wrote:

That has nothing to do with the tools you used.  MatrixEQTL is just calculating correlation, and there is no fancy modeling there.

If something is wrong, that's your dataset.  Have you gone through all the QC steps?  Do you have GWAS/EQTL experience to process genotypes?   

ADD COMMENTlink written 5.7 years ago by Zhenyu Zhang270

Hi all,

I am also using Matrix eqtl and I was wondering which is the best model to run the analysis. Linear model or ANOVA model? Do these models take into consideration if the gene expression data does not follow the normal distribution?

Thank you,


ADD REPLYlink written 5.5 years ago by gisellafiglioli0

If I remember correctly the tutorial for MatrixEQTL provides a snippet of code that transforms expression data for each gene in the expression matrix to a normal distribution. I have the link below. hope that helps

ADD REPLYlink written 4.7 years ago by vakul.mohanty240
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