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Runtime warning by rank_genes_groups

See original GitHub issue

Dear all, I am receiving the following runtime warning when I search for markers within my clusters using

sc.tl.rank_genes_groups

RuntimeWarning: invalid value encountered in log2 rankings_gene_logfoldchanges.append(np.log2(foldchanges[global_indices]))

The warning only happened after I subset my initial clustering and keep few clusters and then again run PCA and HVG analysis on them and do the clustering. It still though run the command and I get the results. Does anyone know why is it happening right after I want to analyze my subset? and is it something that I should worry about ?

Thanks

Issue Analytics

State:
Created 4 years ago
Comments:22 (12 by maintainers)

Top GitHub Comments

2reactions

LuckyMDcommented, May 21, 2019

Maybe rescale yourself then… just add the min expression value per gene to each gene… then you’ll get at least a rebasing of expression values. Relative expression within genes will still be okay.

1reaction

LuckyMDcommented, May 22, 2019

After imputation you don’t have your initial variability in your data. Ideally you have only the biologically relevant variability, but that’s another question. Also, imputation methods take different data as input. Our DCA method takes count data, but MAGIC takes pre-processed data I think.

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