[BioC] edgeR - expressen between genes

[Mark Robinson]

Hi Sridhara.

>> I believe the estimated norm.factor is directly included in the model to test
>> DE, but the values themselves are not modified.

This is correct: the normalization factors are built in as "offsets" in the statistical model, so the count data does not get transformed.

>> My question is if I want to
>> check compare the expression between genes (within a group) what values do I
>> need to consider for this analysis.

Comparing expression b/w genes (as opposed to across conditions for a given gene) is not a standard use case within edgeR (yet) and there are a number of issues that should be dealt with if you want to do this well.  I'm sure others on the list have more experience and can comment more on this, but it seems you need to get a very good handle on gene length (can you always trust the annotation?) and other biases that (e.g. GC content, positional biases) that may introduce differences in read counts that are different from gene to gene.

That said, edgeR has fairly general routines to analyze count data, if you can sort out these other factors.

Cheers,
Mark

On 2011-01-29, at 10:37 AM, Sridhara Gupta Kunjeti wrote:

> Opps I am sorry there is a typo in the subject - expression
> Thanks,
> Sridhara
> 
> 
> 
> On Fri, Jan 28, 2011 at 6:37 PM, Sridhara Gupta Kunjeti
> <sridhara at udel.edu>wrote:
> 
>> Hi All,
>> I am using RNA-seq to study the expression levels of gene globally and as
>> well as group of genes. Plotsmear have given me a meaningful information. I
>> believe the estimated norm.factor is directly included in the model to test
>> DE, but the values themselves are not modified. My question is if I want to
>> check compare the expression between genes (within a group) what values do I
>> need to consider for this analysis. Any help or suggestions will be highly
>> appreciated.
>> 
>> Thanks in advance!
>> Sridhara
>> 
>> 
>> 
>> --
>> Sridhara G Kunjeti
>> PhD Candidate
>> University of Delaware
>> Department of Plant and Soil Science
>> email- sridhara at udel.edu
>> Ph: 832-566-0011
>> 
> 
> 
> 
> -- 
> Sridhara G Kunjeti
> PhD Candidate
> University of Delaware
> Department of Plant and Soil Science
> email- sridhara at udel.edu
> Ph: 832-566-0011
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}