Error when trying to get log fold changes

[hbaker2]

Hello again, I am still having trouble getting the GSEA to work with my single cell RNA sequencing data. Now the trouble I am having is when running this code:

sc.tl.rank_genes_groups(adata_subset
                        groupby='batch',
                        use_raw=False,
                        layer='lognorm',
                        method='wilcoxon',
                        groups=["FP"],
                        reference='FS')

I get the error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_10676\4180658909.py in <module>
----> 1 sc.tl.rank_genes_groups(adata_subset,
      2                         groupby='batch',
      3                         use_raw=False,
      4                         layer='lognorm',
      5                         method='wilcoxon',

~\anaconda3\lib\site-packages\scanpy\tools\_rank_genes_groups.py in rank_genes_groups(adata, groupby, use_raw, groups, reference, n_genes, rankby_abs, pts, key_added, copy, method, corr_method, tie_correct, layer, **kwds)
    588     )
    589 
--> 590     test_obj = _RankGenes(adata, groups_order, groupby, reference, use_raw, layer, pts)
    591 
    592     if check_nonnegative_integers(test_obj.X) and method != 'logreg':

~\anaconda3\lib\site-packages\scanpy\tools\_rank_genes_groups.py in __init__(self, adata, groups, groupby, reference, use_raw, layer, comp_pts)
    115             if use_raw:
    116                 raise ValueError("Cannot specify `layer` and have `use_raw=True`.")
--> 117             X = adata_comp.layers[layer]
    118         else:
    119             if use_raw and adata.raw is not None:

~\anaconda3\lib\site-packages\anndata\_core\aligned_mapping.py in __getitem__(self, key)
    146 
    147     def __getitem__(self, key: str) -> V:
--> 148         return self._data[key]
    149 
    150     def __setitem__(self, key: str, value: V):

KeyError: 'lognorm'

When I take out layer = 'lognorm' from the function, it will run, but I get the warning:

ranking genes
    finished: added to `.uns['rank_genes_groups']`
    'names', sorted np.recarray to be indexed by group ids
    'scores', sorted np.recarray to be indexed by group ids
    'logfoldchanges', sorted np.recarray to be indexed by group ids
    'pvals', sorted np.recarray to be indexed by group ids
    'pvals_adj', sorted np.recarray to be indexed by group ids (0:01:19)
 RuntimeWarning: invalid value encountered in log2
  self.stats[group_name, 'logfoldchanges'] = np.log2(

Then when I try to run
adata_subset.X.max()
I get the output nan

Finally when I try to run

result = adata_subset.uns['rank_genes_groups']
groups = result['names'].dtype.names
degs = pd.DataFrame(
    {group + '_' + key: result[key][group]
    for group in groups for key in ['names','scores', 'pvals','pvals_adj','logfoldchanges']})

I get NaN for all the values in FP_logfoldchanges

Sorry to bother you with this, but your help is much appreciated. Thank you.

[zqfang]

I don't think this is an issue related to GSEApy.

You need to save your lognorm matrix first to make this work

# preprocessing
sc.pp.normalize_total(adata, target_sum=1e4)
sc.pp.log1p(adata)
adata.layers['lognorm'] = adata.X