This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why is Affymetrix computed sex different to that of plink?

Hi

I was wondering if someone can help me interpret the --check-sex results I am getting in plink.

When running this command (./plink --bfile file --check-sex 0.35 0.65 ycount out X) , I seem to get a lot of Problems being detected. I have done this a couple of times and ended up focusing on common snps only as I guess rarer snps can cause problems with F! Ran ycount at the same time (although I am only left with 5 SNPs on the Y chromosome) .

PLINK is detecting 58/162 problems in this relatively small cohort!!! The data came from an Affymetrix chip, and the axiom analysis suite is predicting the gender concordant with the pedigree data provided in all of these!

Here are some of the examples

(see image)table 1 showing snp based gender in plink versus that in affymetrix

Any idea why this is happening?

Thanks

M

axiom analysis suite genotyping plink2
• 3,066 views • link
updated by Mari • Mari • written by HumeMarx • HumeMarx

1 answer

In case anyone is having massive gender inconsistencies in Plink after exporting data from Axiom Analysis Suite: This was because there was an issue in converting the Affy files to PED/MAP format using the Axiom Analysis Suite. Regenerating the files using an upgraded (bug fixed) APT solves the issues.

• 0 views • link
written by HumeMarx • HumeMarx

Which version(s) have the bug and which fixes it?

• 0 views • link
written by h.mon h.mon

Hi I think I might be having the same problem, do you have more details of the APT version you used/conversion steps? Our suppliers initially did this for us but given the weird sex results I don't trust it.

• 0 views • link
written by Mari • Mari

Log in to answer this question.

More posts like this