error in pre rank: ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements

[jimena2]

Hello! I am following the tutorial here:
https://www.youtube.com/watch?v=wIvxFEMQVwg&t=1s

https://github.com/mousepixels/sanbomics_scripts/blob/main/PyDeseq2_DE_tutorial.ipynb

But am getting this error, even when I use the data used in their example.

ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements

input:

pre_res=gp.prerank(rnk=ranking, gene_sets=["GO_Biological_Process_2021"])

Full error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[324], line 1
----> 1 pre_res=gp.prerank(rnk=ranking, gene_sets=[manual_set])

File ~/anaconda3/lib/python3.11/site-packages/gseapy/__init__.py:396, in prerank(rnk, gene_sets, outdir, pheno_pos, pheno_neg, min_size, max_size, permutation_num, weight, ascending, threads, figsize, format, graph_num, no_plot, seed, verbose, *arg, **kwargs)
    375     weight = kwargs["weighted_score_type"]
    377 pre = Prerank(
    378     rnk,
    379     gene_sets,
   (...)
    394     verbose,
    395 )
--> 396 pre.run()
    397 return pre

File ~/anaconda3/lib/python3.11/site-packages/gseapy/gsea.py:444, in Prerank.run(self)
    441 assert self.min_size <= self.max_size
    443 # parsing rankings
--> 444 dat2 = self.load_ranking()
    445 assert len(dat2) > 1
    446 self.ranking = dat2

File ~/anaconda3/lib/python3.11/site-packages/gseapy/gsea.py:418, in Prerank.load_ranking(self)
    415 rank_metric = self._load_data(self.rnk)  # gene id is the first column
    416 if rank_metric.select_dtypes(np.number).shape[1] == 1:
    417     # return series
--> 418     return self._load_ranking(rank_metric)
    419 ## In case the input type multi-column ranking dataframe
    420 # drop na gene id values
    421 rank_metric = rank_metric.dropna(subset=rank_metric.columns[0])

File ~/anaconda3/lib/python3.11/site-packages/gseapy/gsea.py:388, in Prerank._load_ranking(self, rank_metric)
    386 # reset ranking index, because you have sort values and drop duplicates.
    387 rank_metric.reset_index(drop=True, inplace=True)
--> 388 rank_metric.columns = ["gene_name", "prerank"]
    389 rankser = rank_metric.set_index("gene_name", drop=True).squeeze()
    391 # check whether contains infinity values

File ~/anaconda3/lib/python3.11/site-packages/pandas/core/generic.py:6002, in NDFrame.__setattr__(self, name, value)
   6000 try:
   6001     object.__getattribute__(self, name)
-> 6002     return object.__setattr__(self, name, value)
   6003 except AttributeError:
   6004     pass

File ~/anaconda3/lib/python3.11/site-packages/pandas/_libs/properties.pyx:69, in pandas._libs.properties.AxisProperty.__set__()

File ~/anaconda3/lib/python3.11/site-packages/pandas/core/generic.py:730, in NDFrame._set_axis(self, axis, labels)
    725 """
    726 This is called from the cython code when we set the `index` attribute
    727 directly, e.g. `series.index = [1, 2, 3]`.
    728 """
    729 labels = ensure_index(labels)
--> 730 self._mgr.set_axis(axis, labels)
    731 self._clear_item_cache()

File ~/anaconda3/lib/python3.11/site-packages/pandas/core/internals/managers.py:225, in BaseBlockManager.set_axis(self, axis, new_labels)
    223 def set_axis(self, axis: AxisInt, new_labels: Index) -> None:
    224     # Caller is responsible for ensuring we have an Index object.
--> 225     self._validate_set_axis(axis, new_labels)
    226     self.axes[axis] = new_labels

File ~/anaconda3/lib/python3.11/site-packages/pandas/core/internals/base.py:70, in DataManager._validate_set_axis(self, axis, new_labels)
     67     pass
     69 elif new_len != old_len:
---> 70     raise ValueError(
     71         f"Length mismatch: Expected axis has {old_len} elements, new "
     72         f"values have {new_len} elements"
     73     )

ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements

If I run:

import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import gseapy; print(gseapy.__version__)

I get:

3.11.5 (main, Sep 11 2023, 08:31:25) [Clang 14.0.6 ]
CPython
macOS-14.1-arm64-arm-64bit
1.1.1

I thought maybe the GO biological process wasn't downloaded, but I get the same error if I try inputting a manual set of genes.

[zqfang]

can you print the first 5 row of your ranking ? the error message said the input ranking has 3 column

[zqfang]

delete the symbol column, and it will work