hi there, I'd like to thank you for providing an amazing resource for eQTL. https://www.synapse.org/#!Synapse:syn17015233 I'm interested to use eQTL analysis from files » 2.ConsortiumStudies » rnaSeqReprocessing » Analysis I see data for DLPFC ROSMAP, TCX Mayo description provided are excellent for genotype, imputation and initial QC. However, when using matrixEQTL for analysis what was the dosage provided for: A1 or A2 allele? In the output, there is column that tells "expressionIncreasingAllele", it is difficult to harmonize data if I'm to use this with SMR (summary based mendelian randomization). Thank you.

Created by Sanjeev Sariya sanjeevcumc
That helps, thank you :). @sieberts
@sanjeevcumc - The expressionIncreasingAllele" column was included to help aid interpretation, but you'll notice that in the files the expressionIncreasingAllele is the A2 allele when the statistic is positive and is the A1 allele when the statistic is negative. This corresponds to the A2 allele being the reference. Hope that helps. Solly

eQTL analysis: TCX - Mayo, ROSMAP || what is the allele for beta? page is loading…