Hi, I am conducting a meta-analysis and the output doesn't make sense. I ran gwas on several different treatments and some treatments work well, other do not. The effect size for the 3 gwas results are 0.016,0.012 and 0.011 with respective SE of 0.005,0.005,0.004.

However the effect size for the meta-analysis is -0.013 and SE of 0.0025. The effect size of the meta-analysis is of a complete different direction than the gwas's. I ran the gwas using plink and the meta-analysis using METAL. I used the weights effect size estimates using the inverse of the corresponding standard errors. So if the SE are small and all three studies are of similar range, I do not understand why the meta-analysis effect size completely opposite direction. Any help would be much appreciated many thanks!

Are these even statistically significant?

Yes, I've pulled the most significant SNP from the meta-analysis then used that SNP to select from the other studies. I've managed to sort it out - the allele direction was flipped hence the correct absolute effect size but incorrect direction. I'm not sure how that has happened to some files and not all files...