ValueError: zero-size array to reduction operation maximum which has no identity

[panjames]

Encountered when using:

tokens = "GBM_samples", "GBM_controls"
labels = get_unique_annotations(query_tags_annotations(tokens))
labels.annotation.value_counts()

[panjames]

Error output

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-7d153f5dee79> in <module>()
----> 1 combat_matrix, samples  = combat(get_unique_annotations(labels))

/Users/James/Documents/Brain Analysis/star_api/analysis.pyc in combat(df)
    688     df = df.set_index('code')
    689 
--> 690     combined_matrix = combine_matrix(names)
    691     # combined_matrix.to_csv("combined_matrix.csv")
    692     m = drop_missing_samples(combined_matrix).dropna()

/Users/James/Documents/Brain Analysis/star_api/analysis.pyc in combine_matrix(names)
    662         i += 1
    663         print "%s/%s"%(i, len(names)), gse_name, gpl_name
--> 664         median_gene_data = query_median_gene_data(gse_name, gpl_name)
    665         if median_gene_data.empty:
    666             continue

/Users/James/Documents/Brain Analysis/star_api/analysis.pyc in query_median_gene_data(gse_name, gpl_name)
    637             .set_index(['mygene_sym', 'mygene_entrez'])
    638     else:
--> 639         gene_data = query_gene_data(gse_name, gpl_name)
    640         median_gene_data = gene_data \
    641             .reset_index() \

/Users/James/Documents/Brain Analysis/star_api/main.py in query_gene_data(gse_name, gpl_name)
    136     series_id = query_record(gse_name, "series", "gse_name")['id']
    137     platform_id = query_record(gpl_name, "platform", "gpl_name")['id']
--> 138     gene_data = get_gene_data(series_id, platform_id)
    139     gene_data.columns = gene_data.columns + "_" + gpl_name + "_" + gse_name
    140     return gene_data

/Users/James/Documents/Brain Analysis/star_api/main.py in get_gene_data(series_id, platform_id)
    118 
    119 def get_gene_data(series_id, platform_id):
--> 120     data = get_data(series_id, platform_id)
    121     platform_probes = get_platform_probes(platform_id)
    122     gene_data = platform_probes[['mygene_sym', 'mygene_entrez']] \

/Users/James/Documents/Brain Analysis/star_api/main.py in get_data(series_id, platform_id, impute)
     83     elif impute:
     84         data = impute_data(data)
---> 85     data = log_data(data) #logc
     86     data.to_csv("log.data.csv")
     87 

/Users/James/Documents/Brain Analysis/star_api/main.py in log_data(df)
    241 
    242 def log_data(df):
--> 243     if is_logged(df):
    244         return df
    245 

/Users/James/Documents/Brain Analysis/star_api/main.py in is_logged(df)
    250 
    251 def is_logged(df):
--> 252     return np.max(df.values) < 10
    253 
    254 # def is_logged(data):

/Users/James/anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in amax(a, axis, out, keepdims)
   2138     else:
   2139         return _methods._amax(a, axis=axis,
-> 2140                             out=out, keepdims=keepdims)
   2141 
   2142 def amin(a, axis=None, out=None, keepdims=False):

/Users/James/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _amax(a, axis, out, keepdims)
     24 # small reductions
     25 def _amax(a, axis=None, out=None, keepdims=False):
---> 26     return umr_maximum(a, axis, None, out, keepdims)
     27 
     28 def _amin(a, axis=None, out=None, keepdims=False):

ValueError: zero-size array to reduction operation maximum which has no identity

[panjames]

FYI GSE68850 seems to be causing this specific problem.

[zhilongjia]

The Series Matrix File for this GSE68850 does not include content between series_matrix_table_begin and series_matrix_table_end, which means there is no expression values in the Series Matrix File. If so, the solution will be check whether or not get the expression profiles of a certain GSE before continue.