[BioC] is-normalisation-really-required

[Sean Davis]

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

>> 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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