The interpretations

Dr. Jian

Thank you for your response.

I'm going to try find the cause about Question 1.
I will doubt all SNPs are excluded under the condition I used in the

About Question 2, I can understand.
However I have not seen usually such a large chi-squared value.
Can this result be reliable, if data set doesn't contain wrong ??

ks

Dr. Jian

Thank you again for your quick response.

Yes, surely I used a subset of SNPs.

First, I used all SNPs using in the imputation for a SNP-list. However, SE and p-value were large.

Reading topics in this board, I learned small SE was important for correct analyses, and if the number of SNPs was large,and/or sample size was too small, SE tend to be large one.

I think I read a paper suggesting "you need at least 3000 samples for GCTA analyses". Because I used more than 3000 samples and I could not increase samples, I tried to select the SNPs using various ways. The result I paste to this board was one of them, and as you appointed, I selected from GWAS data using the same samples.

Q1) Can't I adjusted the bias by some ways using SNP-list　arbitrarily　selected by GWAS and/or other criteria?
Q2) When the answer is "No I cannot use such list", is it difficult to use GCTA if I cannot increase the sample numbers?