CODEWITHSUNDEEP
rp-valuebonferroni
user1567654
user1567654

Reputation: 47

matrixEQTL R-too many associations

I have used matrixEQTL R package using 1,002,800 SNPs, 29,000 genes and a Bonferroni correction of p-value 1.4e-12. I have 400 samples and used the first five principal components as covariates. It has given 1148000 cis associations and 73136000 trans associations. I have checked other studies with comparative number of genes and SNPs resulting in around 3000 cis and 95000 trans associations. I have used:

me = Matrix_eQTL_main(
snps = snps, 
gene = gene, 
cvrt = cvrt,
output_file_name     = output_file_name_tra,
pvOutputThreshold     = 1.6e-12,
useModel = useModel, 
errorCovariance = numeric(),
verbose = TRUE, 
output_file_name.cis = output_file_name_cis,
pvOutputThreshold.cis = 1.6e-12,
snpspos = snpspos, 
genepos = genepos,
cisDist = cisDist,
pvalue.hist = FALSE,
min.pv.by.genesnp = FALSE,
noFDRsaveMemory = FALSE);

Please help me to understand why I am getting too many associations? Thank you!

Upvotes: 1

Views: 69

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