[BioC] Can DESeq2 find tissue-specific expression genes

Eman Lee [guest] guest at bioconductor.org
Fri Dec 20 04:03:40 CET 2013

Hi, everyone
We want to determine which genes are tissue-specific expression in RNA-Seq data set.
There are 3 samples for each tissue and 10 tissues in total.

For example, we have:
Sample1, Sample2, Sample3
Tissue1, Tissue2,..., Tissue10

How can we use DESeq2 to determine which genes are tissue-specific expression?
Can we take Tissue1 as CASE, other 9 tissues as CONTROL, to find tissue-specific genes (high expression in Tissue1) ?
Eman Lee

 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=Chinese_People's Republic of China.936 
[2] LC_CTYPE=Chinese_People's Republic of China.936   
[3] LC_MONETARY=Chinese_People's Republic of China.936
[4] LC_NUMERIC=C                                      
[5] LC_TIME=Chinese_People's Republic of China.936    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ggplot2_0.9.3.1    plotrix_3.5-2      gplots_2.11.3     
[4] MASS_7.3-29        KernSmooth_2.23-10 caTools_1.14      
[7] gtools_3.1.0       gdata_2.13.2      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6       colorspace_1.2-4   dichromat_2.0-0   
 [4] digest_0.6.4       gtable_0.1.2       labeling_0.2      
 [7] munsell_0.4.2      plyr_1.8           proto_0.3-10      
[10] RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3      
[13] stringr_0.6.2      tools_3.0.0       

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