Hi Richard,
Thank you. It is from taqman real time PCR. I have sent a mail asking how
exactly they normalised the data.
We only have biological replicates and no common reference, so I was told we
can only use Delta CT values.

I make, maybe wrongly, that is Delta Delta CT values are normally
distributed that Delta CT values will also be normally distributed?

I will make plots of the raw data and Delta CT as I know it.





On Fri, May 13, 2011 at 3:53 PM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

> Dear John,
>
>        Is the Delta CT data from PCR or from some other method?
> If it is from PCR in my experience Delta Delta CT is usually normally
> distributed.
> were the first delta references to the difference between the experiment
> and internal reference
> (e.g. GAPDH) and the second delta refers to 2 experimental conditions.
>
> With hopes that the above helps,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman@cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> I am a Bayesian. When I see a multiple-choice question on a test and I
> don't
> know the answer I say "eeney-meaney-miney-moe".
>
> Rose Friedman, Age 14
>
>
>
>
>
>
>
>
> On May 13, 2011, at 10:46 AM, john herbert wrote:
>
>   Dear Bioconductors,
>> I have a bunch of DeltaCT values for several tissues. If I boxplot the
>> data,
>> it looks very similar to microarray data, a lot of congestion around zero.
>>
>> Likewise, if I log2 the data, as in microarray, the distributions looks
>> close to normal and like microarray data.
>>
>> Please see the image here for different plots;
>>
>> https://docs.google.com/leaf?id=0B9IUGsKecS4GNDc0OWVlNzEtZjE5Yi00Y2Q4LWI0M2MtMGFiNzZhMDU0YTFm&hl=en
>>
>> My question is data manipulation in this manner OK for this type of data
>> and
>> will it effect/invalidate any unsupervised machine learning/clustering?
>>
>> Can I quantile normalise the data and still do valid clustering?
>>
>>        [[alternative HTML version deleted]]
>>
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>
>

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