[BioC] question about DESeq or tissue-specific expression

[Wolfgang Huber]

Dear Daofeng

searching for tissue-specific genes is a somewhat different question 
from looking for differential expression.

Many other people may have many different suggestions (and could post 
them here), but a useful starting point for you could be this paper: 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154617/?tool=pubmed#SD1 A 
Gene Expression Barcode for Microarray Data by Michael Zilliox and 
Rafael Irizarry.

In fact, this should be much easier with RNA-Seq data than for 
microarrays. For visualisation / data exploration / density estimation, 
DESeq's variance stabilising transformation could be useful.

	Best wishes
	Wolfgang

Apr/9/12 8:19 PM, Daofeng Li scripsit::
> Dear list members,
>
> I want to ask a question about DESeq or package with similar functionality.
> Can DESeq allow more than 2 samples to used for estimating differential
> expression?
>
> My aim was that If I have tissue A, B and C, and I want to find genes
> specifically high expressed in tissue A. Is there a way to do that by
> DESeq? or other packages?
>
> What if I have 4,5, or 10 tissues? Is it possible to do that?
>
> Thanks in advance for your response.
>
> Best wishes.
> Daofeng


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber