Sunny,

What I meant by "p-value in the disease group is much more significant" is
that the detection call p-value in the disease group are more significant
than healthy group, which means the signal in the disease group is more
significantly above background noise than healthy group.

I am not sure I understand what you mean by "the null", you mean the
background (or the mismatch probes)? When you say "strength of evidence", do
you mean the strength of the signal? Could you be more specific on what
"trouble" means?

Sorry that I get lost here,

-Jack

On Thu, Sep 23, 2010 at 5:43 PM, Sunny Srivastava
<research.baba@gmail.com>wrote:

> Hello Jack,
> I am not sure what you mean by:
>
> "....p-value in the disease group is much more significant
> (say, 1e-10))."
>
> If you mean to use the *magnitude* of p-values as an indicator for the
> *strength* of evidence against (or for) the null, then it it can lead to
> trouble ... Theoretically speaking, it is incorrect to compare two p-values
> and make conclusions about the strength of evidence against (or for) the
> null (in your case *more* differential expression of Gene A in Disease
> compared to Control ).
>
> Thanks and Best Regards,
> S.
>
> 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.
>>
>> 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?
>>
>> Thanks a bunch,
>>
>> -Jack
>>
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>>
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>

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