[BioC] Biological replicates

[Ana Conesa]

There will be always a difference in expression between biological
replicates. If this is big then you need bigger differences between
conditions to find a signigicant differential expressed gene. It´s
not that this will skew the data a bit, it´s that it will be harder
to find significant changes. Big differences between replicates could
have a technical origin or simply reflect biological variation. If
you do not have technical replicates aswell you cannot tell the
difference.
A
>
>
>---- Mensaje Original ----
>De: yogi.sundaravadanam at agrf.org.au
>Para: bioconductor at stat.math.ethz.ch, naomi at stat.psu.edu
>Asunto: Re: [BioC] Biological replicates
>Fecha: Fri, 28 Sep 2007 08:16:09 +1000
>
>>>This is exactly what the t-test is all about.  If you want to state
>
>>that a gene differentially expresses between 2 conditions, don't you
>
>>mean that the difference in expression is higher than the difference
>
>>between biological replicates of the same condition?
>> 
>>I was just wondering what I should do if the difference of
>expression exists between the replicates itself... won't that skew
>the data a bit?  
>>
>>
>> -----Original Message-----
>>From: Naomi Altman [mailto:naomi at stat.psu.edu] 
>>Sent: Friday, 28 September 2007 1:01 AM
>>To: Yogi Sundaravadanam
>>Subject: Re: [BioC] Biological replicates
>>
>>This is exactly what the t-test is all about.  If you want to state 
>>that a gene differentially expresses between 2 conditions, don't you
>
>>mean that the difference in expression is higher than the difference
>
>>between biological replicates of the same condition?
>>
>>--Naomi
>>
>>At 01:13 AM 9/27/2007, you wrote:
>>>Hi all
>>>
>>>
>>>
>>>I am working with biological replicates and I am a bit worried
>about the
>>>biological variation between samples.
>>>
>>>For example, the abundance of a certain gene in sample 1 could be
>>>hundreds of time higher or lower than in sample B. If this is the
>case,
>>>
>>>this will significantly affect the P-value in the t-test.
>>>
>>>
>>>
>>>As such, my question is whether there is a way we can account for
>this
>>>fact in the statistical analysis?
>>>
>>>
>>>
>>>I will be much grateful if you guys could shed some light on this
>topic?
>>>
>>>
>>>
>>>
>>>Thank you
>>>
>>>Yogi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
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>>
>>Naomi S. Altman                                814-865-3791 (voice)
>>Associate Professor
>>Dept. of Statistics                              814-863-7114 (fax)
>>Penn State University                         814-865-1348
>(Statistics)
>>University Park, PA 16802-2111
>>
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>ormatics.conductor
>>