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: http://www.ncbi.nlm.nih.gov/pubmed/21747377 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 analysis). Sean >> >> Thanks, >> ib > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
