Question: eQTL analysis: Genotyping data, microarray expression data
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ngsgene • 370 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.
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modified 5.6 years ago
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Zhenyu Zhang • 270
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6.0 years ago by
ngsgene • 370
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 ?
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.