Calculating Log of the odds (LOD) from Matrix eQTL output
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Entering edit mode
13 months ago
vicky ▴ 30

Hi,

I have got a table of trans-eqtl from matrix eQTL program. The output is:

"snps","gene","beta","t.stat","p.value","FDR","maf"
"2_36751862","IFT88",0.353442498405243,6.69165095948461,9.99397821280154e-07,0.049099454388094,0.0588235294117647

Is there a way to calculate the LOD for these eQTL with matrix eQTL output file?

Thanks!

QTL matrixEQTL • 464 views
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Entering edit mode
13 months ago
LChart 3.9k

There is no way to do this.

The reason is that the odds ratio is only defined for binary (or, more rarely) binomial outcomes. Matrix eQTL uses a quantitative outcome (gene expression, usually TPM or log-transformed TPM).

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