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). [[alternative HTML version deleted]]