Sean,

Thanks for your email. You mean Gene B sounds like a good candidate? Could
you be more specific on the usage of biological replicates? I don't seem to
get the connection to the question I asked.

Thanks,

-Jack

On Thu, Sep 23, 2010 at 5:26 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Thu, Sep 23, 2010 at 4:45 PM, Jack Luo <jluo.rhelp@gmail.com> wrote:
>
>> Hi,
>>
>> This is a conceptual question related to microarray, instead of the usage
>> of
>> any Bioconductor package. I apologize if this bothers anyone.
>>
>> I am struggling to understand the concept of differential expression in
>> terms of its resources (whether it is technical or biological). Suppose I
>> have an experiment with two groups (healthy vs. disease) and try to find
>> some differentially expressed genes, take two genes for example, both of
>> them are differentially expressed (DE) between healthy and disease.
>>
>> Gene A has present detection call for all the samples under study (but the
>> detection call p-value in the healthy group is in the order of 1e-2 ~
>> 1e-3,
>> the detection call p-value in the disease group is much more significant
>> (say, 1e-10)).
>> Gene B has 50% present call in healthy while 100% present call in cancer.
>>
>>
> This sounds like a good candidate.  The gene appears to be differentially
> expressed.
>
>
>> My question is what's the correct interpretation in terms of whether the
>> differential expression is due to technical or biological? Are they both
>> DE
>> due to technical, or A is DE due to biological and B is due to technical,
>> or
>> they are both DE due to biological?
>>
>>
> This is not a question that can be answered with certainty.  However, if
> you used biological replicates, the usual interpretation is that the DE
> could be due to true biological differences (though we cannot prove that
> without further experiments).
>
> Sean
>
>
>

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