[BioC] Summarization by gene or exon or transcript

Steve Lianoglou lianoglou.steve at gene.com
Thu Oct 31 19:13:03 CET 2013

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:


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).


Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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