[BioC] normalization usinf the delta Ct method

[Wolfgang Huber]

Dear Andreia

your question is perhaps too vague to attract people who may want to 
answer it. Can you provide a reproducible example and the output of 
sessionInfo()?

	Best wishes
	Wolfgang

On Sep/10/10 8:55 AM, Andreia Fonseca wrote:
> Dear all,
>
> I have a data set that consists of 36 qPCR plates:
> 3- cond1
> 2-cond 2
> 1-cond3
>
> when I make the normalization using the endogenous gene I get the following
> message:
>
> Calculating deltaCt values
>
>>>          Using control gene(s): U6
>>>          Card 1: Mean=33.62      Stdev=NA
>>>          Card 2: Mean=32.65      Stdev=NA
>
> So after seing the normalized data, I saw that the normalization is just
> making the difference between the Ct of the endogenous gene and the Ct of
> the target gene. Shouldn't the normalization take into account the variance
> of the Ct value of the endogenous gene across all samples and conditions in
> order to normalize and create comparable expression values between
> conditions?
> With kind regrads,
> Andreia
>
>
>
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber