Hi Everyone,
Thanks to recent bioconductor workshop i atteneded ( and of course thanks
to Martin Morgan's inspiration) I am stepping out of hist/plot functions in
R to use bioconductor for more powerful analysis. We have many RNAseq
libries with out replicates. And I read edgeR document and understand, not
much use of doing any significant analysis.

But, now, we are in a position to have biological replicates. But, we are
trying to decide the number. I understand more is merrier. But, what is a
good number? If that is too vaguge to suggest a number....we plan for 4
biological replicates of each condition. Is that good enough ?

Couple more information on the project:
1) Aim of the project is to identify mRNAs that are bound to one
translational factor (compared to another factor)
2) Our organism has 8,000 genes
3) We use a modified RNAseq where each read represents one mRNA transcript.
4) and our library usually contains 10 or more transcript per gene (>80%
cases) per Million mapped reads.
5) this is a first step/survey experiment to see what class of genes
are differentially bound

I appreciate your help/pointers,
If this has been discussed before, could you please point me towards that.

gowthaman


-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

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