[SOLVED] ProbABEL: Which allele is the effective allele?

Questions about ProbABEL are welcome here.
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
wuttke
GenABEL suite user
GenABEL suite user
Posts: 16
Joined: Fri Apr 11, 2014 12:43 pm

[SOLVED] ProbABEL: Which allele is the effective allele?

Postby wuttke » Fri Jun 05, 2015 10:09 am

Hi!

The ProbABEL manual states on page 15 that the A1 allele is the predictor allele.
Now it seems to me the predictor allele frequency given in column 9 of the output is my minor allele frequency, and for the SNP in question A2 is the minor allele.
May it be that the manual is wrong and A2 is the predictor allele?
I assume this does not change with the allele frequency, but is just a convention on which allele to model?

Thanks, best regards, Matthias

wuttke
GenABEL suite user
GenABEL suite user
Posts: 16
Joined: Fri Apr 11, 2014 12:43 pm

Re: ProbABEL: Which allele is the effective allele?

Postby wuttke » Fri Jun 05, 2015 11:28 am

Hi,

I think I solved it by myself.
The perl script I used to convert from Impute2 to (ml)dose format calculates the dosage of A2 instead of A1.
This caused the confusion.

Matthias

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: ProbABEL: Which allele is the effective allele?

Postby lckarssen » Fri Jun 05, 2015 11:54 am

wuttke wrote:I think I solved it by myself.
The perl script I used to convert from Impute2 to (ml)dose format calculates the dosage of A2 instead of A1.
This caused the confusion.

Great! Glad to hear it's resolved.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------


Return to “ProbABEL”

Who is online

Users browsing this forum: No registered users and 2 guests