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?
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
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.
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