decomposition failed error

[prnakka]

Hi, Thanks for making STAAR so easy to install and use! I am trying to run Staar on a test dataset of 5000 individuals for one chromosome and I get the following error when I try to run the STAAR() function:

error: eig_sym(): decomposition failed
Error in STAAR_O_SMMAT(G, P, residuals.phenotype, weights_B = w_B, weights_S = w_S, :
eig_sym(): decomposition failed

Any thoughts on how to resolve this error would be greatly appreciated, thanks!!

[xihaoli]

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

[prnakka]

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

[xihaoli]

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

[prnakka]

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!

[xihaoli]

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