[Bioc-devel] Class for differentially expressed genes?

[Vincent Carey]

On Mon, Mar 9, 2020 at 6:58 AM Roman Hillje via Bioc-devel <
bioc-devel using r-project.org> wrote:

> Hi all,
>
> I was wondering if there is a class for results of differential gene
> expression analysis. I couldn’t find anything generic. Perhaps it’s too
> similar to a simple data frame, but I like the idea of having a consistent
> format. I would imagine something that holds gene names, statistics (logFC,
> p-value, adjusted p-value), plus optional information, e.g. the percent of
> cells expressing a gene (in the context of scRNA-seq). This could then be
> attached to an SCE object (“metadata" slot) to keep all results together.
> I’m probably making things too complicated and should just use a simple
> data frame but wanted to be sure that I’m not missing any existing
> solution. I’d appreciate if you share your advice. Thank you!
>

IMHO it is always profitable to consider the methods desired before
designing a class.  My sense of how this has
proceeded to date starts with limma: data+design -> lmFit -> eBayes ->
topTable(contrast) ... schematically, this has been
an adequate approach to generating and working with DE statistics for some
time.  For DESeq2 a function called
results() is used to acquire statistics on DE.

There are aspects of asking for and interpreting results DE analyses that
could be made more systematic and
perhaps shared among packages so that users have a more consistent and
informative experience in this
domain ... sketching out the key actions may be the place to start.  Just
my 2c.


> Cheers,
> Roman
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