eQTL analysis: Genotyping data, microarray expression data
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.
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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?
you can
plink --recode12and then process that output with your favorite language: R/Python/Perl. I have just used a one liner awk loop to do it.You need to click "add reply" to post a response to the comments above, instead of commenting to the main post.
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.