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qRT-PCR calculations


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#1 moerae

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Posted 17 September 2009 - 03:40 PM

Hi,

I have no idea if this has been covered by another thread or not, but I'll post this up here anyways. I've done qRT-PCR on zebrafish samples and have analysed three biological replicates separately using qBase and I've found that the general trend across all three replicates are the same. To try and make presenting this easier I've averaged across all three replicates (geometric mean) and the standard error across the board is quite big probably because the expression levels between the three runs are quite big. Does anyone know of a way to calculate the average and eliminate biological differences between the replicates so that the standard error isn't actually reflecting the biological differences?

I hope I've worded this so that people can understand.

#2 Dr Teeth

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Posted 18 September 2009 - 04:05 AM

Hi,

I have no idea if this has been covered by another thread or not, but I'll post this up here anyways. I've done qRT-PCR on zebrafish samples and have analysed three biological replicates separately using qBase and I've found that the general trend across all three replicates are the same. To try and make presenting this easier I've averaged across all three replicates (geometric mean) and the standard error across the board is quite big probably because the expression levels between the three runs are quite big. Does anyone know of a way to calculate the average and eliminate biological differences between the replicates so that the standard error isn't actually reflecting the biological differences?

I hope I've worded this so that people can understand.


Have you tried a paired t test? Paired tests are good when samples from different replicates vary in absolute value, but show similar trends (e.g. a two fold increase with treatment).

Science is simply common sense at its best that is rigidly accurate in observation and merciless to fallacy in logic.
Thomas Henry Huxley

#3 moerae

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Posted 18 September 2009 - 03:02 PM

Thanks. I'll give that a try.




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