Hi,
When I call fitLMM, I get this:
`AttributeError Traceback (most recent call last)
in ()
7
8 # fit lmm without correction
----> 9 pv0,beta0,info0 = sclvm.fitLMM(K=None,i0=i0,i1=i1,verbose=False)
10 pv0,beta0,info0 = hack_fitLMM(sclvm, K=None,i0=i0,i1=i1,verbose=False)
11 # fit lmm with correction
/usr/lib/python2.7/site-packages/scLVM/core.pyc in fitLMM(self, K, tech_noise, idx, i0, i1, verbose)
333 else:
334 _K = None
--> 335 lm = QTL.test_lmm(Ystd,Ystd[:,ids:ids+1],K=_K,verbose=False,**lmm_params)
336 pv[count,:] = lm.getPv()[0,:]
337 beta[count,:] = lm.getBetaSNP()[0,:]
AttributeError: 'module' object has no attribute 'test_lmm'`
I'm using limix version 1.0.18, but previously tried it with 2.0.2 and had the same problem. The problem seems to be that scLVM calls QTL.test_lmm() when it should be calling QTL.qtl_test_lmm(). I think that test_lmm() was renamed.
Thanks and cheers.
Urbs
Hi,
When I call fitLMM, I get this:
`AttributeError Traceback (most recent call last)
in ()
7
8 # fit lmm without correction
----> 9 pv0,beta0,info0 = sclvm.fitLMM(K=None,i0=i0,i1=i1,verbose=False)
10 pv0,beta0,info0 = hack_fitLMM(sclvm, K=None,i0=i0,i1=i1,verbose=False)
11 # fit lmm with correction
/usr/lib/python2.7/site-packages/scLVM/core.pyc in fitLMM(self, K, tech_noise, idx, i0, i1, verbose)
333 else:
334 _K = None
--> 335 lm = QTL.test_lmm(Ystd,Ystd[:,ids:ids+1],K=_K,verbose=False,**lmm_params)
336 pv[count,:] = lm.getPv()[0,:]
337 beta[count,:] = lm.getBetaSNP()[0,:]
AttributeError: 'module' object has no attribute 'test_lmm'`
I'm using limix version 1.0.18, but previously tried it with 2.0.2 and had the same problem. The problem seems to be that scLVM calls QTL.test_lmm() when it should be calling QTL.qtl_test_lmm(). I think that test_lmm() was renamed.
Thanks and cheers.
Urbs