[BioC] RNA-Seq fold change compared to control, without replicates

[Steve Lianoglou]

Hi,

On Tue, Dec 17, 2013 at 1:27 PM, Lisa Cohen
<lisa.johnson.cohen at gmail.com> wrote:
> I am analyzing a set of RNA-Seq data without replicates, possibly
> using edgeR. (We understand limitations and are only interested in
> descriptive analyses.) There are three different treatments (OC, OD,
> UD) and one control (UC).
>
> For each treatment, I want to find transcripts with highest and lowest
> fold changes compared to the control. What is the best way to do this?

Have you read through the user's guide that comes with edgeR?

http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

There's lots of very useful stuff to be learned there w.r.t analyses
of RNA-seq data, so you should definitely do so.

There is even a section entitled "What do do if you have no
replicates." If you still have questions after you've read through
that guide, then please post with specific questions regarding
particular steps of the analysis you are having trouble with.

If you are new to these types of analyses, reading through the user
guides that come with limma and DESeq2 will be very informative as
well, and highly recommended.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech