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Question: Missing design when using Scran to create a DESeqDataSet
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gravatar for berry14
6 weeks 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 6 weeks ago by Aaron Lun17k • written 6 weeks ago by berry140
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gravatar for Aaron Lun
6 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

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

ADD COMMENTlink written 6 weeks ago by Aaron Lun17k

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 6 weeks 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 6 weeks ago • written 6 weeks ago by Aaron Lun17k

Yes, you are right. That works. Thanks!

And I agree the bare minimum is a cleaner solution.

ADD REPLYlink written 6 weeks ago by berry140
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