[BioC] qPCRnorm

Heidi Dvinge heidi at ebi.ac.uk
Fri Jan 8 09:44:49 CET 2010

Hello Andreia,

I'm not familiar with qpcrBatch objects, but <shameless self plug> if
you're interested in testing for differential expression between genes,
you could also consider the HTqPCR package. The raw data is read into a
qPCRSet object, which is similar to ExpressionSets used for microarray
data. The package performs various normalisations of the raw qPCR data,
similar to qpcrNorm, along with some data visualisation and filtering.
Differential expression can be analysed using a standard t-test or with a
limma-based approach, or if you want to do something else than that you
can extract all the values from your qPCRSet object using exprs().
</shameless self plug>


> Dear list,
> I am trying to understand how qpcrNorm works, so I followed the
> documentation, so I understood how to normalize the data, but now I want
> to
> test which genes are differentially expressed between batches and make a
> Mann-Whitney U-test. How can I transform the normalized data which is a
> object class qpcrBatch into a data.frame. Or else how can test using this
> kind of object.
> Thanks for the help
> Andreia
> 	[[alternative HTML version deleted]]
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