eQTL analysis: Genotyping data, microarray expression data

Question

[ngsgene]

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.

[NB]

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?

[Zhenyu Zhang]

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.

[ngsgene]

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[ngsgene]

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.