ComBat Error

[Zifeng-L]

Hi, here. After learning, I tried to use my own data to analysis. Everything went well before the batch correction. And I couldn't understand what happened and how to debug. Can anyone help me? Thx! `

ComBat batch correction

sc.pp.combat(adata, key='sample')

Standardizing Data across genes.

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AssertionError Traceback (most recent call last)

in () 1 # ComBat batch correction ----> 2 sc.pp.combat(adata, key='sample') ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/scanpy/preprocessing/_combat.py in combat(adata, key, covariates, inplace) 210 # standardize across genes using a pooled variance estimator 211 logg.info("Standardizing Data across genes.\n") --> 212 s_data, design, var_pooled, stand_mean = _standardize_data(model, data, key) 213 214 # fitting the parameters on the standardized data ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/scanpy/preprocessing/_combat.py in _standardize_data(model, data, batch_key) 103 n_array = float(sum(n_batches)) 104 --> 105 design = _design_matrix(model, batch_key, batch_levels) 106 107 # compute pooled variance estimator ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/scanpy/preprocessing/_combat.py in _design_matrix(model, batch_key, batch_levels) 37 "~ 0 + C(Q('{}'), levels=batch_levels)".format(batch_key), 38 model, ---> 39 return_type="dataframe", 40 ) 41 model = model.drop([batch_key], axis=1) ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/highlevel.py in dmatrix(formula_like, data, eval_env, NA_action, return_type) 289 eval_env = EvalEnvironment.capture(eval_env, reference=1) 290 (lhs, rhs) = _do_highlevel_design(formula_like, data, eval_env, --> 291 NA_action, return_type) 292 if lhs.shape[1] != 0: 293 raise PatsyError("encountered outcome variables for a model " ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/highlevel.py in _do_highlevel_design(formula_like, data, eval_env, NA_action, return_type) 163 return iter([data]) 164 design_infos = _try_incr_builders(formula_like, data_iter_maker, eval_env, --> 165 NA_action) 166 if design_infos is not None: 167 return build_design_matrices(design_infos, data, ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/highlevel.py in _try_incr_builders(formula_like, data_iter_maker, eval_env, NA_action) 60 "ascii-only, or else upgrade to Python 3.") 61 if isinstance(formula_like, str): ---> 62 formula_like = ModelDesc.from_formula(formula_like) 63 # fallthrough 64 if isinstance(formula_like, ModelDesc): ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/desc.py in from_formula(cls, tree_or_string) 162 tree = tree_or_string 163 else: --> 164 tree = parse_formula(tree_or_string) 165 value = Evaluator().eval(tree, require_evalexpr=False) 166 assert isinstance(value, cls) ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/parse_formula.py in parse_formula(code, extra_operators) 146 tree = infix_parse(_tokenize_formula(code, operator_strings), 147 operators, --> 148 _atomic_token_types) 149 if not isinstance(tree, ParseNode) or tree.type != "~": 150 tree = ParseNode("~", None, [tree], tree.origin) ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/infix_parser.py in infix_parse(tokens, operators, atomic_types, trace) 208 209 want_noun = True --> 210 for token in token_source: 211 if c.trace: 212 print("Reading next token (want_noun=%r)" % (want_noun,)) ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/parse_formula.py in _tokenize_formula(code, operator_strings) 92 else: 93 it.push_back((pytype, token_string, origin)) ---> 94 yield _read_python_expr(it, end_tokens) 95 96 def test__tokenize_formula(): ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/parse_formula.py in _read_python_expr(it, end_tokens) 42 origins = [] 43 bracket_level = 0 ---> 44 for pytype, token_string, origin in it: 45 assert bracket_level >= 0 46 if bracket_level == 0 and token_string in end_tokens: ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/util.py in next(self) 319 else: 320 # May raise StopIteration --> 321 return six.advance_iterator(self._it) 322 __next__ = next 323 ~/anaconda2/envs/cnmf_env/lib/python3.6/site-packages/patsy/tokens.py in python_tokenize(code) 33 break 34 origin = Origin(code, start, end) ---> 35 assert pytype not in (tokenize.NL, tokenize.NEWLINE) 36 if pytype == tokenize.ERRORTOKEN: 37 raise PatsyError("error tokenizing input " AssertionError: `

[LuckyMD]

Hi,

Does you anndata object have the obs column 'sample'? Could you show the output of just writing adata in your console?

[Zifeng-L]

你好

您的andata对象是否具有该obs列'sample'？您能否显示仅adata在控制台中编写的输出？

AnnData object with n_obs × n_vars = 23120 × 25905 obs: 'sample', 'sample_id', 'n_counts', 'log_counts', 'n_genes', 'mt_frac', 'size_factors' var: 'gene_id', 'n_cells' uns: 'sample_colors', 'log1p' layers: 'counts'

[LuckyMD]

Could you try running adata.obs['sample'] = adata.obs['sample'].astype('category') and then running again?

[Zifeng-L]

adata.obs['sample'] = adata.obs['sample'].astype('category')

I tried recently, unluckily, the error was still exist.

[LuckyMD]

This is quite strange. Do your samples all cover multiple cells, or is there some samples without any cells remaining after filtering? It would be helpful if you had a minimal reproducible example for this. Can you reproduce this error with for example sc.datasets.pbmc68k_reduced()?

[LuckyMD]

Given no further replies, I will close this issue.