[BioC] which one should I choose in DEseq
anders at embl.de
Fri Jan 3 11:08:41 CET 2014
On 03/01/14 04:23, liyue [guest] wrote:
> I have a RNA-seq dataset.
> The format is:
> gene_id day0 day2 day6 day9
> mmu-let-7a-5p 3862 456 650 4991
> mmu-let-7b-5p 462 222 97 56
> mmu-let-7c-5p 13081 777 724 1953
> mmu-let-7d-5p 12357 679 729 5017
> I just want to find the differentially expressd genes during four days. Which one can I choose in DEseq?
> 3.1 between two experimental conditions
> 3.2 working partially without replicates
> 3.3 working without sny replicates
If you want advice on how to analyze your data, you need to tell us what
_exactly_ you want to do. What is the experimental design? What is the
biological question? What do _you_ mean by "differentially expressed
I point this out because there is no one single way to analyse RNA-Seq
data, especially not when time series are involved.
I'm also bit puzzled by your question. You do not have replicates and
you have already found out that there is a section "working without any
replicates". Also, you have _four_ time point, so the section "between
_two_ experimental conditions" is clearly not applicable.
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