Error in the result file

[netwon123]

Hi developer,
I used your script to calculated the log2afc of my eqtl data. Fortunately, it worked and got results, but the values are both the upper limit and the lower limit. Could you give me some advice? Thank you very muck!

Here's my code
python aFC.py --vcf jx_268_miss01_maf005_biallele.phased2.vcf.gz --pheno cecum.expr_tmm_inv4_afc.bed.gz --qtl cecum_cis.cis_qtl.txt.gz.txt --o aFC_cecum_log2afc.txt --cov covariate_cecum.txt --boot 100 --log_xform 0

[Russell-07]

I also encountered the same problem as you, but I don't know how to solve it

[netwon123]

I also encountered the same problem as you, but I don't know how to solve it

I have solved it. You should use the raw expression, like TMM, TPM or other. Don't normalized it.

[Russell-07]

I will try it ，thanks！