Hi, 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 Thanks a lot! Best, Liyue -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 [7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

Dear Liyue 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 genes"? 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. Simon