[BioC] Biological replicates

[Jenny Drnevich]

Hi Yogi,

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'm not sure what your question is... the fact that a large amount of 
biological variation among samples in one treatment group will affect 
the P-value in a t-test is EXACTLY how the statistical analysis 
accounts for a large amount of biological variation.  In simplified 
terms, a t-test calculates the differences in the means between two 
groups, then adjusts for the amount of biological variation within 
each group. The p-value is the probability of getting the calculated 
t-value if the two groups had been randomly sampled from the same 
distribution.  A low probability leads to the conclusion that the two 
groups were likely sampled from distributions with different means.

If this doesn't answer your question, perhaps you could elaborate on 
exactly how you want to account for biological variation in the 
statistical analysis?

Cheers,
Jenny




>
>
>I will be much grateful if you guys could shed some light on this topic?
>
>
>
>
>Thank you
>
>Yogi
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at uiuc.edu