Hi Simon, thank you again for your help. I'll try to explain the idea of
the experiment.

Basically we want to know what happen in tense of expression when you
over-express a gen, for example oct2, while mouse development.
To do that, we insert a gene construction with a promoter + oct2 gene. This
promoter is sensible to a drug, so when you add the drug, oct2 is expressed.
This drug is added at different times , from 4 days to 7, from 6 days to 9
and from 8 days to 11. These are my MTcD mice ( mutant + drug ). I have
also mutants mice with no drug (MTsD).

So, if I don't take into account, at this moment, the time course and I
start to analyze the data from the 9.5 days, I look for DEG from MTcD vs
MTsD.
At the end of this analysis, I have DEG for two different reasons :
   Oct2 overexpression
   Drug effect

So, in order to remove the possible effect of adding the drug, we have
another different kind of mouse (they don't have the gene construction to
overexpress oct2) that we can use. So we have a wild type mouse that has
been treated with the same drug at the same days of the MTcD. We call it,
WTcD. And of course we have also a WT mouse with no drug treatment (WTsD).
So comparing the WTcD vs WTsD, I can infer the possible effect of the drug
and I'd like to remove this effect from my mutants. More or less like :

  (MTsD - MTcD) - (WTsD -WTcD) = Real effect of the overexpression.

Do you know how to do that ?

Again thanks for your help.




2013/6/3 Simon Anders <anders@embl.de>

> Hi Eduardo
>
>
> On 03/06/13 20:41, Eduardo Andrés León wrote:
>
>> Your suggestion at the end of the mail, was my starting point (MTsD vs
>> MTcD). But in this case I was loosing the effect that the drug could add
>> to the model.
>>
>> The only problem here is to remove the effect of the drug (That I can
>> infer from the comparison between WTsD vs WTcD. But this also add a new
>> variable ... the mice).
>>
>
> Sorry, you lost me now. I thought mutation and mouse stain are aliased?
>
> What biological question do you want to address? We need some more details
> here; an abstract discussion won't lead anywhere.
>
>   Simon
>



-- 
===================================================
Eduardo Andrés León
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054)
e-mail: eandres@cnio.es        Fax: (+34) 91 224 69 76
Unidad de Bioinformática       Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029                Zip Code: 28029
C/. Melchor Fernández Almagro, 3    Madrid (Spain)
http://bioinfo.cnio.es    http://bioinfo.cnio.es/people/eandres
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