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dtsoucas / DWLS

Gene expression deconvolution using dampened weighted least squares
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Error in solveDampenedWLS() #8

Open RK1912 opened 3 years ago

RK1912 commented 3 years ago

Hi

I am using raw count data from single cell RNA-seq and bulk RNA-seq. I am currently stuck at running the deconvolution function solveDampenedWLS(). I get the error : 

Error in solve.QP(D, d, A, bzero) :
  matrix D in quadratic function is not positive definite!

I tried to solve this using nearPD() to get the nearest positive definite matrix for the data , but I still get the same error.

Can you suggest a way I can fix this issue?

Thanks a lot!

annavpo commented 3 years ago

Hi

I am using raw count data from single cell RNA-seq and bulk RNA-seq. I am currently stuck at running the deconvolution function solveDampenedWLS(). I get the error :

Error in solve.QP(D, d, A, bzero) :
  matrix D in quadratic function is not positive definite!

I tried to solve this using nearPD() to get the nearest positive definite matrix for the data , but I still get the same error.

Can you suggest a way I can fix this issue?

Thanks a lot!

Hello,

I ran into the same error. Did you find any solution to that? Thanks

kunstner commented 2 years ago

Hi, I solved this issue using

solution<-solve.QP(D,d,A,bzero, factorized = TRUE)$solution

instead of

# solution<-solve.QP(D,d,A,bzero)$solution

Best