On Wed, Oct 3, 2012 at 9:11 PM, i b <ibse...@gmail.com> wrote:
> Dear all,
> how reliable is running Cuffdiff without replicates? e.g.one samples
> agains another one?
>
> Is it statistically makign any difference when using replicates?

Seqanswers might be a better place to ask this very interesting
technical question that goes way beyond Galaxy...

My 2c: Statistically speaking, sequencing and biology are both noisy.
Replicates provide information about non-experimental (technical and
biological) variation. That variation is usually not the variation you
are looking for, but if you want to remove it, you have to model it
and that requires information from replicates (or really good
guesswork). In some situations (eg extreme experimental conditions),
I'm sure you'll find biologically meaningful signal without them but
in my experience, they can really help to decrease non-experimental
noise, particularly where the experimental condition induces only
subtle changes in transcript abundance.

You could always analyse a data set with replicates and compare the
results with and without those replicates yourself to see what happens
- it would be a nice paper I'm sure.

>
> Thanks,
> ib
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