Question: eQTL analysis: Genotyping data, microarray expression data
0
gravatar for ngsgene
5.0 years ago by
ngsgene350
United States
ngsgene350 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 • 2.9k views
ADD COMMENTlink modified 4.6 years ago by Zhenyu Zhang260 • written 5.0 years ago by ngsgene350

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 4.7 years ago by Nandini840

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 4.6 years ago by ngsgene350
1
gravatar for Zhenyu Zhang
4.6 years ago by
Zhenyu Zhang260
United States
Zhenyu Zhang260 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 4.6 years ago by Zhenyu Zhang260

You need to click "add reply" to post a response to the comments above, instead of commenting to the main post.

 

 

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by ngsgene350
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