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Question: Error invalid class "SummarizedExperiment" when using library("MultiDataSet")
gravatar for s.w.vanderlaan
17 months ago by
s.w.vanderlaan20 wrote:


I have two SummarizedExperiments: one is methylation and the other RNAseq data. I'd like to combine it using the MultiDataSet library to be able to run linear regression models between methylation and RNAseq data.

I've combined the two SE's into one, using the code below:

multi <- createMultiDataSet()
multi <- add_rse(multi, 
                  dataset.type = "450KData", warnings = FALSE)
multi <- add_rse(multi, 
                            dataset.type = "RNAseqData", warnings = FALSE)


# Select common samples, and datasets
multi.common <- commonSamples(multi)

# Obtain the original objects
multi.mset <- multi[["450KData"]]

This all seems to work without events. But than, when I try: multi.eset <- multi[["RNAseqData"]] to get the expression dataset, it throws an error:

Error in validObject(.Object) : 
  invalid class “SummarizedExperiment” object: 
  nb of rows in 'assay' (14332) must equal nb of rows in 'rowData' (466311)

How should I interpret this? And more importantly, how do I fix it? Indeed, there are 14,332 genes, and 466,311 exons among those 14,332 genes.



ADD COMMENTlink modified 17 months ago • written 17 months ago by s.w.vanderlaan20

Hi Sander,

I am not able to reproduce your error with the info that you gave me. Could you post the traceback and sessionInfo?



ADD REPLYlink written 17 months ago by carlos.ruiz0
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