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berry14
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@berry14-14096
Last seen 6.6 years ago
The Scran vignette indicates the SCESet object can be convert to an object for DESeq2 analysis. http://bioconductor.org/packages/devel/bioc/vignettes/scran/inst/doc/scran.html
Once it converted, it's already an DESeqDataSet, yet without a design. it's not obvious to me how to add a design to this DESeqDataSet.
Any suggestion is welcome. Thanks.
In DESeq2, the design is added when setting up the object using various methods, such as
When Scran convert SCESet to DESeqDataSet, the count matrix is converted directly to DESeqDataSet. I was not able to find an option to add design?
You can just add it afterwards with
design(dds) <- formula(...), assuming your factors are incolData. I don't want to add more arguments toconvertTothan the bare minimum, otherwise the interface becomes unwieldy (a handful of package-specific arguments for each output class adds up to a lot of arguments in the final function). It is easier for everyone if package-specific operations are performed outside ofconvertToon the returned object.Yes, you are right. That works. Thanks!
And I agree the bare minimum is a cleaner solution.