Hello,
I am new to analysing RNA-seq data. I try to construct a SummarizedExperiment object for counts and metadata. On the tutorial, it only mentioned that "Often, SummarizedExperiment or RangedSummarizedExperiment objects are returned by functions written by other packages. " Does anyone know what other packages can be used for constructing SummarizedExperiment object?
Thank you for your reply! But there are only procedures for creating DESeqDataSetFromTximport in the vignette, which seems not the SummarizedExperiment object I want. I do not quite understand what does this mean: The object you create inherits from the SummarizedExperiment class, and you can create it easily.
The vignette has procedures for four different input types, not just one! You can use a matrix of counts, or use
tximport
or an existingSummarizedExperiment
object, or HT-Seq counts.The
dds
object inherits fromSummarizedExperiment
, and it was easy to make from a matrix of counts and adata.frame
describing the data. Any object that inherits fromSummarizedExperiment
will act like aSummarizedExperiment
so you don't have to care that it's actually aDESeqDataSet
if you want to treat it like aSummarizedExperiment
.Hi James, thank you for your detailed explanation! Very clear!