getEnrichedPathways error in scan(file...

[IsmaelMP86]

HI, First of all thank you for this incredible pacage/app. It s really usefull to easily show analysis to non r code users. I am my self still not a fully skilled person on R. When using cerebro1.3, adn following your guide, I don't riched to get enriched pathways as an error is occurring:

14:47:35] Found 2 groups: sampleID, namedClusters
[14:47:35] Get enriched pathways for group `sampleID`...
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  la ligne 1 n'avait pas 2 éléments
...etc

Did i make a mistake somewhere? cerebri_seurat is here and head is the folowwing

my_samplesl@misc[["marker_genes"]][["cerebro_seurat"]]
#         namedClusters  gene   p_val         avg_log2FC  pct.1  pct.2  p_val_adj
# genes1  C0             gene1  0.000000e+00  5.9129553   1.000  0.204  0.000000e+00

thanks in advance for you help. kind regards

[romanhaa]

Hi @IsmaelMP86!

I'm not sure what causes this error, but my guess is that either (1) the format of marker genes returned by Seurat has changed or (2) it has to do with parsing the response from Enrichr (which is the service used internally to perform pathway enrichment analysis). Unfortunately, I don't have the time anymore to work on cerebroApp so I won't be able to help you any further with this. Since the source code is all public, you could try to debug this yourself (it might be a good occasion to practice and learn).

Cheers, Roman