Comments (2)
I have the same error
python = 3.11
pandas = 2.0.3
code :
gene_symbols = ['GNAI1', 'SPP1', 'IKZF1', 'TGFBR2', 'TLR4', 'MBOAT7', 'CCNB2', 'MYLK', 'CDKN1A', 'ZNF586', 'WASHC4', 'SRC', 'UGDH', 'CDK6', 'HMG20B']
gp.enrichr(gene_list=gene_symbols, gene_sets="GO_Biological_Process_2023", outdir=None)
It seems to be an error related to pandas. Maybe it could be corrected by using pandas.concat() instead of pandas.DataFrame.append() ?
AttributeError Traceback (most recent call last)
/tmp/ipykernel_98143/1600401673.py in ?()
----> 1 gp.enrichr(gene_list=gene_symbols, gene_sets="GO_Biological_Process_2023", outdir=None, )
~/miniconda3/envs/dataproc/lib/python3.11/site-packages/gseapy/enrichr.py in ?(gene_list, gene_sets, description, outdir, cutoff, format, figsize, top_term, no_plot, verbose)
299 :return: An Enrichr object, which obj.res2d contains your enrichr query.
300 """
301 enr = Enrichr(gene_list, gene_sets, description, outdir,
302 cutoff, format, figsize, top_term, no_plot, verbose)
--> 303 enr.run()
304
305 return enr
~/miniconda3/envs/dataproc/lib/python3.11/site-packages/gseapy/enrichr.py in ?(self)
169 shortID, res = self.get_results(genes_list)
170 # Remember gene set library used
171 res["Gene_set"] = self._gs
172 # Append to master dataframe
--> 173 self.results = self.results.append(res, ignore_index=True)
174 self.res2d = res
175 sleep(2)
176 if self._outdir is None: continue
~/miniconda3/envs/dataproc/lib/python3.11/site-packages/pandas/core/generic.py in ?(self, name)
...
5987 ):
5988 return self[name]
-> 5989 return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'
from gseapy.
Hello, could you please update GSEApy to the latest version? This should fix the issue we are currently experiencing. Thank you.
from gseapy.
Related Issues (20)
- Prerank fails with list of gene sets HOT 1
- `log2_ratio_of_classes` required number of samples in the group >=3 HOT 6
- key error HOT 5
- Using a count matrix with NA values for GSEApy HOT 1
- 'DataFrame' object has no attribute 'append' HOT 2
- Could not return matplotlib.Axes in python script HOT 2
- Only last one used when params `gene_sets` is given as list HOT 2
- is it able to change the order of cls item HOT 3
- Missing wheels for Python 3.12 on PyPI HOT 2
- Prerank function not reading gmt files correctly HOT 2
- gseaplot how to do to reset the label/NES etc. font size and set the FDR display HOT 1
- The difference between input gene symbol name and geneID HOT 1
- Missing one input gene into Prerank module HOT 1
- Running gp.enrich() with custom gene_sets throwing error. HOT 3
- New implementation of gseapy and gseaplot() HOT 4
- Enrichment_map Top_term Param Inconsistencies HOT 1
- dotplot legend label error HOT 1
- gene sets score and gsva
- high memory consumption when using gsva HOT 2
- dotplot AttributeError
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