Question: RNAseq scater error in plotQC()
0
gravatar for Vladimir Krasikov
15 months ago by
Vladimir Krasikov90 wrote:

Dear creators/maintainers of the scater package

First of all, thanks for slim and intuitive package for the scRNAseq data

It is my first go with scRNAseq data and I try to follow scater vignettes

 

Looks like there might be a little bug in plotQC()

It happened that  my SingleCellExperiment object has only 'logcounts' data (no original 'counts)

when calling first:

sce <- calculateQCMetrics(sce, exprs_values = "logcounts")

and then

plotQC(sce, type = "highest-expression", exprs_values = "logcounts")

an error appears:

Error in .qc_hunter(object, "total_features_by_counts", mode = "column") : 
  failed to find 'total_features_by_counts' in column metadata

 

Looks like that despite  "total_features_by_logcounts" plotQC still requires  'total_features_by_counts'

Fix needed

Thanks

scater scrnaseq plotqc • 283 views
ADD COMMENTlink modified 15 months ago by Aaron Lun25k • written 15 months ago by Vladimir Krasikov90
Answer: RNAseq scater error in plotQC()
0
gravatar for Aaron Lun
15 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

Thanks for the bug report. This will be fixed in the latest version of scater. In the meantime, you can manually set the colour_cells_by argument to "total_features_by_logcounts" to avoid the error.

ADD COMMENTlink modified 15 months ago • written 15 months ago by Aaron Lun25k
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