[BioC] Summarization by gene or exon or transcript

[Steve Lianoglou]

Hi Reema,


On Thu, Oct 31, 2013 at 10:04 AM, Reema Singh <reema28sep at gmail.com> wrote:
> Dear All,
>
> I would like to known in order to find out the differentially expressed
> genes between two condition - what is the idea feature for summarization? .
> I have choosen gene by summarization. Is this a good choice?.
>
> Any suggestions would be very helpful.

You're going to have to ask a more specific question, as I'm having a
hard time understanding what you are after.

If you are just curious how you could perform a differential
expression analysis, there are workflows you can read through here:

http://bioconductor.org/help/workflows/

Different packages that perform these analyses are also very well
documented, including:

* The limma user's guide: this can be applied to both microarray and
rna-seq analysis
* edgeR user's guide: differential rna-seq expression
* DESeq2 vignette: differential rna-seq expression
* DEXSeq vignette: differential exon usage using rna-seq data
* oligo: different types of array analyses (including expression,
tiling, and exon arrays)
* xps: similar types of analyses to oligo (I think).

Enjoy,
-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech