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Question: Missing design when using Scran to create a DESeqDataSet
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gravatar for berry14
12 months ago by
berry140
berry140 wrote:

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.

ADD COMMENTlink modified 12 months ago by Aaron Lun21k • written 12 months ago by berry140
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gravatar for Aaron Lun
12 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:

It seems like ?design would be a good place to start.

ADD COMMENTlink written 12 months ago by Aaron Lun21k

In DESeq2, the design is added when setting up the object using various methods, such as

DESeqDataSetFromTximport, DESeqDataSetFromHTSeqCount, DESeqDataSetFromMatrix, or DESeqDataSet

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?

ADD REPLYlink written 12 months ago by berry140
1

You can just add it afterwards with design(dds) <- formula(...), assuming your factors are in colData. I don't want to add more arguments to convertTo than 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 of convertTo on the returned object.

ADD REPLYlink modified 12 months ago • written 12 months ago by Aaron Lun21k

Yes, you are right. That works. Thanks!

And I agree the bare minimum is a cleaner solution.

ADD REPLYlink written 12 months ago by berry140
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