How to setup a Summarized Experiment

Question

[Sethzard]

I'm starting from a count matrix called Raw Dreads with each column being an RNA-Seq dataset, and each row being the reads associated with a gene (the names are EnsemblIDs).

I've also created matrix called support with the columns: sample, the name of an RNA-Seq dataset, and condition, which is the dataset they belong to.

I want to use EnrichmentBrowser on this dataset, and so need to turn it into an SummarizedExperiment file. I can't for the life of me work out how. Can anyone give me advice?

Answer 1

[ATpoint]

Where is the problem or rather at which point of the manual did you get stuck?

The first step is to initialize the object with counts, e.g.:

data.se <- SummarizedExperiment(list(counts=as.matrix(your.counts)))

Check the manual and then report where the problem is: https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

[Sethzard]

That worked, and also worked with adding colData=Support. I think I got confused because the command that's listed didn't work:

SummarizedExperiment(assays=list(counts=counts), colData=colData)

Sorry if I missed something, but it didn't seem obvious.