decomposition failed error about staar HOT 5 CLOSED

Hi Priya,
Thanks for your question. In STAAR(), the eig_sym() is a c++ function embedded in the Armadillo library that performs eigen-decomposition of the underlying dense symmetric matrix (in this case, the weighted covariance matrix). May I ask what would be the dimension for your eigen-decomposition, i.e. what is the dimension of the G matrix (you may follow lines 76-102 in the STAAR() function to obtain this G matrix from the input genotype matrix)?
Best,
Xihao

from staar.

Hi, The dimension of the G matrix I was running this function on was 4620 x 285. Thanks, Priya

from staar.

Hi Priya,
Thanks for your reply. The dimension of your G matrix is manageable for STAAR() function. In this case, could you please check whether your G matrix or annotation weights, i.e. w_B, w_S, w_A, contain any missing values? If not, could you please try updating your Rcpp and RcppArmadillo packages to the latest version and try it again?
Best,
Xihao

from staar.

Hello, Removing variants with missing values in the annotations fixed the problem for me, thank you so much!! I had one last question: is there a method you would recommend to combine STAAR p-values across multiple studies? Thank you again!

from staar.

Hi Priya,

Thanks so much for letting me know that the problem has been fixed. For your question on combining STAAR p-values, could you please send us an email to have a further discussion, as it may depend on the specific study design of your project?

Thanks again.

Best,
Xihao

from staar.