Calculating Log of the odds (LOD) from Matrix eQTL output

Question

[vicky]

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!

Answer 1

[LChart]

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).