insightsengineering / insightsengineering/teal.modules.hermes
[Bug]: Uncaught error in Quality Control module
- Dominant language
- R
- Stars
- 7
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
In [RNA-seq app](https://genentech.shinyapps.io/nest_rna-seq_main/):
+ Quality Control tab:
+ Select Experiment - hd1
+ Plot Type - Top Genes Plot
+ Selected Assay - any
+ Gene Filter Settings - ON
+ Minimum CPM - ~20-30k
+ Minimum CPM Proportion - 0.2-0.6
`Error: Problem during calculation of variance-stabilized transformation (VST), try again with more genes. More details: Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space`
If this error is expected, use a validation mechanism to capture it.
Contributor guide
Research direction
Reproduce the RNA-seq app workflow in the Quality Control tab with experiment hd1, Top Genes Plot, any assay, and the stated Gene Filter Settings. Trace how the VST calculation error is handled; done means the expected error is captured by validation instead of remaining uncaught. No source file or test is named in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100