Hi Heidi,

Thanks for the advise. I am going through the HTqPCR documentation but I am
getting the following error while trying to read the sample input data:

path <- system.file("exData", package = "HTqPCR")
> head(read.delim(file.path(path, "files.txt")))
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file '/files.txt': No such file or directory
> files <- read.delim(file.path(path, "files.txt"))
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file '/files.txt': No such file or directory


I am working in a windows machine and using R 2.9.2

thanks
Andreia

On Fri, Jan 8, 2010 at 8:44 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> 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>
>
> Cheers
> \Heidi
>
> > 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
> >
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> >
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>
>
>

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