Why are my eigenvalues coming out negative for my positive definite covariance matrix?

I have a 51 x 51 covariance matrix that is derived from historic forward rates that is positive definite. I know it is because in Python np.cholesky returns a correct cholesky decomposition. However, when I use the eigh function to return the eigenvalues/vectors, about half of the eigenvalues are negative, which makes no sense. The data is imported from excel using pandas dataframes, then I make a covariance matrix using:

CovMat2 = np.cov(df.T)*252/10000

Then I request the eigenvalues with

eig_vals, eig_vecs = np.linalg.eigh(CovMat2)
print('Eigenvectors \n%s' %eig_vecs)
print('\nEigenvalues \n%s' %eig_vals)
and I get this output:

Eigenvalues
[-1.35963506e-03 -1.09487110e-03 -5.00507744e-04 -4.76180253e-04
-4.26481890e-04 -3.65765795e-04 -3.21245207e-04 -2.90812021e-04
-2.49174935e-04 -2.47519558e-04 -2.20946393e-04 -2.11019230e-04
-2.01940366e-04 -1.99581473e-04 -1.87201389e-04 -1.74938799e-04
-1.41441186e-04 -1.24247169e-04 -1.11167101e-04 -9.78191552e-05
-8.75246993e-05 -8.69367038e-05 -8.36134890e-05 -8.03187245e-05
-7.36730798e-05 -5.70815773e-05 -4.65981850e-05 -2.92229574e-05
-2.77958421e-05 -1.84175309e-05 -7.45464337e-06  1.37165843e-05
2.91872261e-05  3.93959482e-05  4.46749803e-05  6.07783927e-05
7.42504887e-05  7.99764211e-05  9.49821563e-05  1.05894570e-04
1.15379642e-04  1.37420008e-04  1.47812090e-04  2.07834453e-04
2.63958555e-04  2.75403037e-04  3.01136833e-04  3.06428511e-04
3.75549199e-04  1.96296188e-03  5.80951459e-03]

which makes no sense. What am I doing wrong? Perhaps it's something to do with converting dataframes to a numpy matrix?

• Does your covariance matrix look as you expect it to? Can you share a snippet? – Scott Skiles Jul 7 '18 at 15:40
• The values in the covariance matrix are small because it's calculated on the differences in interest rates in a time series but yes I'm positive that it's correct – M Thomas Jul 7 '18 at 16:36
• Eigenvectors can be negative, much of your post mentions negative eigenvalues but in your text you specifically say eigenvectors (a mistype I think). If np.cholesky returns a decomposition, and your matrix is truly symmetric, then the only remaining option for negative eigenvals is numerical precision. Is your dtype 'float64'. – Attack68 Jul 7 '18 at 19:34
• You're right, that was a typo, I meant the eigenvalues are negative. I haven't specified the data type, maybe I'll try that – M Thomas Jul 7 '18 at 22:19
• datatype is float64 – M Thomas Jul 7 '18 at 23:27