Error running RMarkdown templates

[kokyriakidis]

In the QC template I get an error when it tries to run

plotMeanSD(object)

Commenting this line runs the report fine.

In the DGE template I get an error when it tries to run

design(dds) <- params$design

It throws

Error in validObject(object) : invalid class "DESeqDataSet" object: all variables in design formula must be columns in colData

I used the bcb.rda file located in the data folder in this repo.

[mjsteinbaugh]

Hi @kokyriakidis, try running this code and see if the plot renders:

library(bcbioRNASeq)
data(bcb, package = "bcbioRNASeq")
plotMeanSD(bcb)

And to double check, which version of bcbioRNASeq are you using?

packageVersion("bcbioRNASeq")
## [1] '0.3.29'

I think you're hitting an error with the DESeq2 template because you haven't set the design in the YAML params at the top of the R Markdown correctly. Look for this part:

  ## Design formula must contain columns defined in `colData()`.
  design: !r formula("~ group")

You can specify any type of DESeq design formula there, as long as it matches the metadata in colData(dds). Refer to the DESeq2 vignette for details on how this works. Here are some examples:

• Simple contrast: ~ treatment
• Genotype/treatment interaction: ~ genotype + treatment + genotype:treatment

[mjsteinbaugh]

Also for debugging the plotMeanSD() error, try setting these options before running that function and post the error message in the thread:

# requires rlang package to be installed
options(
    "error" = quote(rlang::entrace()),
    "rlang_backtrace_on_error" = "full",
    "rstudio.errors.suppressed" = FALSE
)

[kokyriakidis]

> packageVersion("bcbioRNASeq")
[1] '0.3.29'

Still get an error at plotMeanSD()

> options(
+     "error" = quote(rlang::entrace()),
+     "rlang_backtrace_on_error" = "full",
+     "rstudio.errors.suppressed" = FALSE
+ )
> 
> data(bcb, package = "bcbioRNASeq")
> 
> plotMeanSD(bcb)
Error in .local(object, ...) : Assert failure.
[1] requireNamespace("vsn", quietly = TRUE) is not TRUE.
<error/rlang_error>
Assert failure.
[1] requireNamespace("vsn", quietly = TRUE) is not TRUE.
Backtrace:
    █
 1. ├─bioverbs::plotMeanSD(bcb)
 2. └─bcbioRNASeq::plotMeanSD(bcb)
 3.   └─bcbioRNASeq:::.local(object, ...)
 4.     └─goalie::assert(...)
<parent: error/simpleError>
Assert failure.
[1] requireNamespace("vsn", quietly = TRUE) is not TRUE.

[mjsteinbaugh]

Ah okay you need to install the vsn package:

BiocManager::install("vsn")

[mjsteinbaugh]

@kokyriakidis I'm closing this issue due to inactivity. If the recommendation above didn't work, please comment and I'll reopen.