[BioC] which one should I choose in DEGseq

[liyue [guest]]

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 DEGseq?

5.1 Example for DEGexp
5.2 Example for DEGseq
5.3 Example for samWrapper
5.4 Examplle for getGeneExp


Thanks a lot!

Best,

Liyue

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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=C                 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 

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