[BioC] RNA degradation problem

[fhong@salk.edu]

Hi Matthew,

Thank you very much for your help.

> It's amazing how many
> lab plant biologists see pooled samples from a bulk of plants grown at
> the same time as biological replicates when they are clearly not.
I would think that all plants under experiment shoudl be grown at the same
time without different conditions/treatments. Biological replicates should
be tissue samples from differnt groupd of plants, say sample from 50
plants as replicate1 and sample from another 50 as replicate 2.
Do you think that biological replicates should be grown at different time?


> I find hist, RNA deg, AffyPLM and a simple RMA norm followed by
> plot(as.data.frame(exprs(eset.rma))) can answer in most cases for why it
> didn't work, or won't work - in the rare case when someone asks for QC
> before rather than after they realise the data is strange ;-)
This actually pull out another question: when % of differential genes is
large, which normalization better works better?

http://cactus.salk.edu/temp/QC_t.doc
Take a look at the last plot, which clearly indicate homogeneous within
replicates and heterogeneous among samples.
(1) Will stem top and stem base differ so much? Or it is the preparation
process bring in extra correlaton within replicates.
(2) when % of differential genes is large, which normalization better
works better?

many thanks!
Fangxin




--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105