Fixation of Bug (reported by Kai)

tgac-vumc · May 4, 2021 · 242aa73 · 242aa73
1 parent b85f06a
commit 242aa73
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Showing 17 changed files with 5 additions and 5 deletions.
diff --git a/Deconvolution/BLADE.py b/Deconvolution/BLADE.py
@@ -180,7 +180,7 @@ def grad_Nu(Y, SigmaY, Nu, Omega, Beta, Mu0, Alpha0, Beta0, Kappa0, Ngene, Ncell
     NuExp = np.sum(Nu, 0)/Nsample
 
     Diff = np.zeros((Ngene, Ncell))
-    ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \
+    ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \
             Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0))
 
     for i in range(Nsample):
@@ -278,13 +278,13 @@ def grad_Omega(Y, SigmaY, Nu, Omega, Beta, Mu0, Alpha0, Beta0, Kappa0, Ngene, Nc
     # gradient of PX (first term)
     AlphaN = Alpha0 + Nsample * 0.5
     NuExp = np.sum(Nu, 0)/Nsample
-    ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \
+    ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \
             Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0))
 
     for i in range(Nsample):
         ExpBetaN = ExpBetaN + 0.5*np.square(Nu[i,:,:] - NuExp)
 
-    Nominator = - AlphaN * Nsample*(Nsample+3)*Omega + Kappa0 /(Kappa0 + Nsample) * Omega
+    Nominator = - AlphaN * (Nsample-1)*Omega + Kappa0 /(Kappa0 + Nsample) * Omega
     grad_PX = Nominator / ExpBetaN
 
 
@@ -565,7 +565,7 @@ def Estep_PX(Mu0, Nu, Omega, Alpha0, Beta0, Kappa0, Ncell, Nsample):
     NuExp = np.sum(Nu, 0)/Nsample # expected Nu, Ngene by Ncell
     AlphaN = Alpha0 + 0.5*Nsample # Posterior Alpha
 
-    ExpBetaN = Beta0 + Nsample*(Nsample+3)/2*np.square(Omega) + \
+    ExpBetaN = Beta0 + (Nsample-1)/2*np.square(Omega) + \
             Kappa0*Nsample/(2*(Kappa0 + Nsample)) * (np.square(Omega)/Nsample + np.square(NuExp - Mu0))
 
     for i in range(Nsample):

diff --git a/LICENSE b/LICENSE
diff --git a/PGFdeconvolution/LogNormalvsNB_TCGA.R b/PGFdeconvolution/LogNormalvsNB_TCGA.R
diff --git a/PGFdeconvolution/LogNormalvsNB_TCGA.html b/PGFdeconvolution/LogNormalvsNB_TCGA.html
diff --git a/PGFdeconvolution/README.md b/PGFdeconvolution/README.md
diff --git a/PGFdeconvolution/TCGA-MESO.RData b/PGFdeconvolution/TCGA-MESO.RData
diff --git a/PGFdeconvolution/TCGA-SARC.RData b/PGFdeconvolution/TCGA-SARC.RData
diff --git a/PGFdeconvolution/install.R b/PGFdeconvolution/install.R
diff --git a/PGFdeconvolution/source_estmusigmadist2.R b/PGFdeconvolution/source_estmusigmadist2.R
diff --git a/README.md b/README.md
diff --git a/Singularity b/Singularity
diff --git a/data/.keep b/data/.keep
diff --git a/environment.yml b/environment.yml
diff --git a/framework.png b/framework.png
diff --git a/jupyter/BLADE - Demo script.ipynb b/jupyter/BLADE - Demo script.ipynb
diff --git a/logo_final_small.png b/logo_final_small.png
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="BLADE-Deconvolution",
-    version="0.0.5",
+    version="0.0.6",
     author="Yongsoo Kim",
     author_email="[email protected]",
     description="BLADE (Bayesian Log-normAl DEconvolution)",