[BioC] is-normalisation-really-required

[Gorjanc Gregor]

> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: sre 2005-04-13 14:16
> To: Gorjanc Gregor
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] is-normalisation-really-required
>  
> On Apr 13, 2005, at 8:03 AM, Gorjanc Gregor wrote:
> 
> > Hi!
> >
> > You might try analysis with and without normalization and take
> > a look at the results. If they say the same thing than I would
> > say, no it is not necessary to do normalization.
> >
> 
> So, if the two results agree, then the results with normalization are  
> correct; if not then the results with normalization are still correct.   
> Sounds like we are pretty much stuck with normalization....
> 
> Sean
Why should one do normalization if the results aren't different. But, in
that case it really does not matter and one can do it or not.


>> dear friends
>> i have situation, where i thought its ok for me not to
>> do normalisation, i am afraid i may be wrong. i want
>> your advice in this regard.
>>
>> we performed a wild type - mutant, dye-swap
>> experiment.
>> when we analysed the intensity values, they were
>> consistant among the two experiment (dye-swap). ie.,
>> almost same values for mutants in both the experiments
>> of the dye-swap.
>> since the values are almost same, i thought there
>> might not be any dye-bias, so i just went ahead,
>> averaged the two values, found out their ratio and
>> filtered genes with 2 fold change.
>>
>> so i have done this without normalisation.
>> i am afraid, i might be wrong, my 2 fold chaging genes
>> might be wrong...
>> kindly give me your advice in this regard.
>> i did analyse the data with limma, but the topTable
>> genes there never correlates with my 2 fold genes.
>>
>> kindly correct me.
>> thanks
>>
>> vijay
>> graduate student
>> department of biological sciences
>> the university of southern mississippi
>> MS, USA
>
> --
> Lep pozdrav / With regards,
>     Gregor Gorjanc
>
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