the meaning of "NA" in plink meta-analysis result

Question

[lanjinglingxiaoni]

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.

[tarumuranen]

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?

[ATpoint]

Please use ADD COMMENT / REPLY not the answer field. OP did not log in for > 5 years, better not wait for an answer.

Answer 1

[chrchang523]

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.

[lanjinglingxiaoni]

thank you very much. +qt is important