GlmpcaError: for count data, the minimum value must be >=0

[ondina-draia]

Hello,

I'm trying to run PASTE2 to align two MERFISH slices but an error occured:

GlmpcaError Traceback (most recent call last)
Cell In[34], line 1
----> 1 pi_12 = PASTE2.partial_pairwise_align(slice_wt1_D, slice_wt2_D, s=0.7)

File ~/Documents/merfish_lames/p30/analysis/tutorials/stagate_base_2/lib/python3.9/site-packages/paste2/PASTE2.py:260, in partial_pairwise_align(sliceA, sliceB, s, alpha, armijo, dissimilarity, use_rep, G_init, a_distribution, b_distribution, norm, return_obj, verbose)
258 M = pca_distance(sliceA, sliceB, 2000, 20)
259 elif dissimilarity.lower() == 'glmpca':
--> 260 M = glmpca_distance(A_X, B_X, latent_dim=50, filter=True, verbose=verbose)
261 else:
262 print("ERROR")

File ~/Documents/merfish_lames/p30/analysis/tutorials/stagate_base_2/lib/python3.9/site-packages/paste2/helper.py:82, in glmpca_distance(X, Y, latent_dim, filter, verbose)
79 joint_matrix = joint_matrix[:, top_indices]
81 print("Starting GLM-PCA...")
---> 82 res = glmpca(joint_matrix.T, latent_dim, penalty=1, verbose=verbose)
83 #res = glmpca(joint_matrix.T, latent_dim, fam='nb', penalty=1, verbose=True)
84 reduced_joint_matrix = res["factors"]

File ~/Documents/merfish_lames/p30/analysis/tutorials/stagate_base_2/lib/python3.9/site-packages/paste2/glmpca.py:325, in glmpca(Y, L, fam, ctl, penalty, verbose, init, nb_theta, X, Z, sz)
323 # sanity check inputs
324 if fam in ("poi", "nb", "mult", "bern") and np.min(Y) < 0:
--> 325 raise GlmpcaError("for count data, the minimum value must be >=0")
326 if fam == "bern" and np.max(Y) > 1:
327 raise GlmpcaError("for Bernoulli model, the maximum value must be <=1")

GlmpcaError: for count data, the minimum value must be >=0

When running: pi_12 = PASTE2.partial_pairwise_align(slice_wt1_D, slice_wt2_D, s=0.7)

My data looks like this in terms of structure:

AnnData object with n_obs × n_vars = 21284 × 960 obs: 'fov', 'volume', 'center_x', 'center_y', 'min_x', 'min_y', 'max_x', 'max_y', 'anisotropy', 'transcript_count', 'perimeter_area_ratio', 'solidity', 'region', 'slide', 'dataset_id', 'cells_region', 'EntityID' var: 'mean', 'std' uns: 'log1p', 'spatialdata_attrs' obsm: 'blank', 'spatial'

My minimum transcript counts by gene is 20 (I don't know if it's relevant)

Those are my slices.

What should I do? Where is the error coming from?

[x-h-liu]

Sorry for the late reply. I think this means the transcript count matrix has a negative value.