vidger vsBoxPlot error with DESeq2 dataset
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bbj23 • 0
@bbj23-23693
Last seen 3.8 years ago

I'm trying some first-pass exploratory analyses of a DESeq2 dataset using vidger. Naturally, I get an error with my very first graph.

I created the dataset using tximport, and did a basic analysis:

deseqdat<-DESeqDataSetFromTximport(mytxi, colData = samples.df, design = ~ treatment)
mydds<-DESeq(deseqdat)
myresults<-results(mydds, contrasts = c("treatment", "A", "B"))

I've tried to make box plots using vidger to view FPKM distributions:

library(vidger)
vsBoxPlot(mydds, d.factor = "treatment", type = "deseq")

This is just as described in the vidger vignette. It works with the DESeq2 pasilla dataset example, but not for my own data, which gives an error:

Error in names(ls.mean) <- sapply(nam, paste) : 
  'names' attribute [2] must be the same length as the vector [0]

It's not clear to me where in the vsBoxPlot function this error is popping up, and I'm really at a loss what the issue is with my data. Is there something (embarrassingly simple) I've missed?

Thanks for any help!

vidger • 395 views
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