[BioC] Manual creation of Affybatch object to study highthrouput qPCR experiments.

[Heidi Dvinge]

Hi Ali,

> Hi Ali,
>
> On 10/20/2011 2:49 AM, Ali Mo [guest] wrote:
>> Hi every one.
>>
>> I am using 384 well qPCR array for miRNA study. I wanted to normalize my
>> results using affy. How can I create an affybatch wich contains my Cq
>> values? Thanks a lot.
>
> You don't want to do this. Trying to stuff qPCR data into an AffyBatch
> is asking for trouble. Quantile normalizing qPCR data is asking for
> trouble as well, IMO, but they are your data.
>
In case you want to try some other normalisation methods, including e.g.
geometric mean which has been recommended for miRNA data, then you might
want to have a look at the HTqPCR package. If you type

library(HTqPCR)
vignette("HTqPCR")

that should give you enough instructions on how to start, if you're not
too familiar with Bioconductor. There's also a brief comparison of 4-5
different normalisaiton methods, including quantile.

HTH
\Heidi

> If you want to quantile normalize these data, use normalizeQuantiles()
> from the limma package.
>
> Best.
>
> Jim
>
>
>>
>> PS. I am new to R/bioconductor.
>>
>>   -- output of sessionInfo():
>>
>> No R command!
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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