insightsengineering / insightsengineering/teal.modules.hermes

[Bug]: Uncaught error in Quality Control module

Open
#318 1 comment 0 reactions 0 assignees View on GitHub
bug low-priority
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

Open the contributing 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

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