vst counts are not defined in object.

[tiger815]

Hi,

When I try to analyze my samples using this pipeline, the following error occurs in PlotPCA.

plotPCA(object1, label = FALSE) ℹ Using vst counts. Error in h(simpleError(msg, call)) : error in evaluating the argument 'args' in selecting a method for function 'do.call': vst counts are not defined in object.

Samples were successfully loaded with the following options.

GeneID, normalization

object1 <- bcbioRNASeq( uploadDir = "/data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/", level = "genes", organism = "Homo sapiens", genomeBuild = "hg38", fast = TRUE )

Could you give me some advice?

Many thanks,

[mjsteinbaugh]

Thanks I'll take a look. What version of bcbioRNASeq are you currently using? Note that VST counts don't get calculated with the fast = TRUE option, so this error is expected. However, I'll work on improving the error message for plotPCA in this case.

[mjsteinbaugh]

For reference, here's a minimal reprex:

library(bcbioRNASeq)
uploadDir <- system.file("extdata/bcbio", package = "bcbioRNASeq")
object <- bcbioRNASeq(uploadDir = uploadDir, fast = TRUE)
plotPCA(object)

[mjsteinbaugh]

Improved the error message regarding this issue in the pending v0.3.37 release. Thanks for the heads up!