On Wed, Oct 3, 2012 at 7:35 AM, Ross <ross.laza...@gmail.com> wrote:
> 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.
A bit off-topic, but you might take a look here:
In short, one needs replication in biology, regardless of the
technology used. In particular, one would never suggest running a
microarray experiment without replicates; one should follow
approximately the same rules for sequencing (and sequence data
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