[BioC] Can DESeq2 find tissue-specific expression genes
Eman Lee [guest]
guest at bioconductor.org
Fri Dec 20 04:03:40 CET 2013
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) ?
-- output of sessionInfo():
R version 3.0.0 (2013-04-03)
Platform: i386-w64-mingw32/i386 (32-bit)
 LC_COLLATE=Chinese_People's Republic of China.936
 LC_CTYPE=Chinese_People's Republic of China.936
 LC_MONETARY=Chinese_People's Republic of China.936
 LC_TIME=Chinese_People's Republic of China.936
attached base packages:
 grid stats graphics grDevices utils datasets methods
other attached packages:
 ggplot2_0.9.3.1 plotrix_3.5-2 gplots_2.11.3
 MASS_7.3-29 KernSmooth_2.23-10 caTools_1.14
 gtools_3.1.0 gdata_2.13.2
loaded via a namespace (and not attached):
 bitops_1.0-6 colorspace_1.2-4 dichromat_2.0-0
 digest_0.6.4 gtable_0.1.2 labeling_0.2
 munsell_0.4.2 plyr_1.8 proto_0.3-10
 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3
 stringr_0.6.2 tools_3.0.0
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