opened
DorothyWen1
username_0
Hi there,

I am interested in using your program to analyse my data. However, when I used default setting, I get errors when the number of SNPs within the region is larger than the sample size. I checked regionsRanker.py. It looks to me that  the problems are due to the below code. Could you please let me know how to fix this? Thanks. 

 def eigenDecompose(self, X, K, normalize=True):
                if (X.shape[1] >= X.shape[0]):
                              s,U = la.eigh(K)


Cherry
When X.shage[1]>X.shape[0]
issue
created
omerwe
username_1
Hi Cherry,

Thanks for trying out MKLMM! Can you please provide more details about the
exact command you ran and the error message you received? Having a larger
number of SNPs in a region than the sample size shouldn't lead to a problem
(typically one region includes the entire genome), but I'm afraid it could
use up a lot of memory, unless they are linear kernels. Is this related to
what you're seeing?

Thanks,

Omer
comment
created
omerwe
username_1
Hi Cherry,

Can you successfully run the examples shown in the github page
<https://github.com/username_1/MKLMM>? If yes, then I would guess that there's
some specific problem with your data, and it's very difficult for me to
figure out what it is without more information... My best guess is that
your input includes a region that doesn't have any SNPs (e.g., maybe all
the SNPs were filtered out for some reason)? But I would need to see the
data or to get more information (or at least to see the error output) to
know more.

Best,

Omer
comment