Direction of the fixed effect

Hello,

Many thanks for your reply! Having checked the new post gcta.freeforums.net/thread/211/estimating-fixed-effects-gcta-greml, we found that there are still some mismatches between the new information and the old information that we got before. In out analysis we have 22 quantitative covariates (20PCs+age+age2)input by using --qcovar and 2 binary covariates(sex and another binary variable) input by using --covar. Having run --reml combined with --reml-est-fix, there are 25 lines of fixed effect (the lines starting below the line:Fix_eff SE) in the .hsq file. According to your new post, "If we have a quantitative covariate and a categorical covariate, the mean term will also be ignored", then we should have 26 lines of fixed effect estimated (22 lines for quantitative covariates and 4 lines(2X2) for binary covariates). Or if each of the binary covariates only takes one line, then we should have 24 lines in total, if so it seems that the first line should represent mean term(Although I don't understand how it is made)? 

Also in another thread gcta.freeforums.net/thread/129/adding-random-effect-reml we get a slightly different answer:

Dec 11, 2014 12:54:50 GMT 1 zhihong said:
Hi Asling,

1. The first row should be miu, population mean, 2. then quantitative covariates, 3. discrete covariates are at the bottom if you have.

Cheers,
Zhihong

So I am not sure in the output *hsq file (1) if miu (mean) is listed in the first line and (2)if each binary covariate takes one line.

Thanks,

Asling