Question: eQTL analysis: Genotyping data, microarray expression data
gravatar for ngsgene
6.0 years ago by
United States
ngsgene370 wrote:

After referring to some posts on Biostars am leaning towards using Matrix eQTL for eQTL analysis using genotyping data (plink format) and microarray expression data (either analyzed through Partek or R packages) 

Am looking for some blog posts / user experiences of having done something similar, I have looked at the tutorial Matrix eQTL has but anything more detailed or leading to further insight into understanding analytical steps/process/results is much appreciated!

Thanks for suggestions.



eqtl plink partek R matrix eqtl • 3.4k views
ADD COMMENTlink modified 5.6 years ago by Zhenyu Zhang270 • written 6.0 years ago by ngsgene370

hey, did you manage to run MatrixEQTL using genotype data ? I am trying to do the same, but unable to convert the large datasets into MatrixEQTL format.. how did you manage to do that with plink files ?

ADD REPLYlink written 5.7 years ago by Nandini890

Wrote a script to parse the plink output, MatrixEQTL needed the genotype coded as either 0,1,2 - using both alleles that you get in the plink file you can account for ref ref/ref alt/alt alt and generate the genotype input file.

ADD REPLYlink written 5.6 years ago by ngsgene370
gravatar for Zhenyu Zhang
5.6 years ago by
Zhenyu Zhang270
United States
Zhenyu Zhang270 wrote:

you can plink --recode12

and then process that output with your favorite language: R/Python/Perl

I have just used a one liner awk loop to do it. 

ADD COMMENTlink written 5.6 years ago by Zhenyu Zhang270

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ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by ngsgene370
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