Hi,
I use the meta-analysis function in PLINK to meta analyze two cohorts.
For example
Cohort1:
SNP CHR BP pvalue beta se
rs7412 19 45412079 4.80e-13 -.544908 .0753598
Cohort2
SNP CHR BP pvalue beta se
rs7412 19 45412079 9.67e-17 -1.03076 .124057 .
When I use plink --noweb --meta-analysis file1.assoc file2.assoc + no-allele,
the results in plink.meta are NA.
Could anyone tell me why it appeared as NA? How could I get the exact p value in such case?
Thank you very much.
•
written
by
lanjinglingxiaoni •
I believe PLINK requires the pvalue column label to be "P", the beta column label to be "BETA" (in caps), and the standard error column label to be "SE". You also need to specify the qt modifier after the + sign, so that PLINK knows to expect a BETA instead of an OR column.
•
written
by
chrchang523
thank you very much. +qt is important
•
written
by
lanjinglingxiaoni •
Log in to answer this question.
Could you provide and example, where you give both qt and no-allele after + sign, please? Is there a white-space or something else between the parameters?
Please use
ADD COMMENT / REPLYnot the answer field. OP did not log in for > 5 years, better not wait for an answer.