Unusual error when running gseapy.prerank

[hbaker2]

Hello, I am analyzing single cell RNA sequencing data using GSEApy and am getting an unusual error when trying to run:

res = gp.prerank(rnk=gene_rank, gene_sets='GO_Biological_Process_2021')

KeyError: "'de novo' posttranslational protein folding (GO:0051084)"

Even when I change it to a different gene set, I get a different weird error:

res = gp.prerank(rnk=gene_rank, gene_sets='KEGG_2016')

KeyError: 'Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate Homo sapiens hsa00532'

My gene_rank list was generated fine though, that part worked. Your help is much appreciated.

[zqfang]

Could you send me the full trackback error message? I can't help without more context

[hbaker2]

Here is the entire output, your help is much appreciated:

2023-01-09 14:58:18,205 [WARNING] Input gene rankings contains NA values(gene name and ranking value), drop them all!
2023-01-09 14:58:18,298 [WARNING] Duplicated values found in preranked stats: 24.72% of genes
The order of those genes will be arbitrary, which may produce unexpected results.
2023-01-09 14:58:18,388 [ERROR] No gene sets passed through filtering condition !!!
Hint 1: Try to lower min_size or increase max_size !
Hint 2: Check gene symbols are identifiable to your gmt input.
Hint 3: Gene symbols curated in Enrichr web services are all upcases.

---

KeyError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_5408\3554385580.py in
----> 1 res = gp.prerank(rnk=gene_rank, gene_sets='GO_Biological_Process_2021')

~\anaconda3\lib\site-packages\gseapy_init_.py in prerank(rnk, gene_sets, outdir, pheno_pos, pheno_neg, min_size, max_size, permutation_num, weighted_score_type, ascending, threads, figsize, format, graph_num, no_plot, seed, verbose, *arg, **kwarg)
355 verbose,
356 )
--> 357 pre.run()
358 return pre
359

~\anaconda3\lib\site-packages\gseapy\gsea.py in run(self)
424 self._logger.info("Parsing data files for GSEA.............................")
425 # filtering out gene sets and build gene sets dictionary
--> 426 gmt = self.load_gmt(gene_list=dat2.index.values, gmt=self.gene_sets)
427 self.gmt = gmt
428 self._logger.info(

~\anaconda3\lib\site-packages\gseapy\base.py in load_gmt(self, gene_list, gmt)
233 )
234 self._logger.error(msg)
--> 235 dict_head = "{ %s: [%s]}" % (subsets[0], genesets_dict[subsets[0]])
236 self._logger.error(
237 "The first entry of your gene_sets (gmt) look like this : %s"

KeyError: "'de novo' posttranslational protein folding (GO:0051084)"

[zqfang]

It complains the gene identifiers are not matched to the GMT file. Are your gene_rank's gene_symols all upcases ?

[hbaker2]

Thank you, it worked once I capitalized the gene names!