RNA Report is failing with too few samples.

[slsevilla]

Problem

RNA report is failing when running only two samples. This is because the DGEList part of the report is expecting more samples to produce downstream graphics like the PCA.

processing file: rNA_flowcells.Rmd
Quitting from lines 26-83 (rNA_flowcells.Rmd)
Error in prcomp(t(as.matrix(deg_voom$E)), scale. = T)$x[, 1:3] :
  subscript out of bounds
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
In addition: Warning message:
In filterByExpr.DGEList(deg) :
  All samples appear to belong to the same group.

Solution

Update the report to either skip this feature, take in a group file (this used to be part of the pipeline) or use each sample as an individual 'group'.

[kopardev]

is this still happening with 2.6.1??

[kelly-sovacool]

is this still a problem with 2.6.1? will check with just 2 samples