[BioC] qPCRnorm

[Heidi Dvinge]

Hi Andreia,

well, sadly enough that's because I'm a numpty!! When I wrote the
function(s), rather than defining file position using file.path, I just
concatenated names with "/" because at that point I was only intending on
using this function for myself on my mac.

On mac/linux this can be fixed for readCtData by having the data you want
to read in a different directory than your current working directory.
However, for windows you'll need a bug-fixed version of readCtData(). I
have this available, but it hasn't been submitted to the BioC devel
repository yet - it's creeping rapidly higher up on my to-do list. If you
want, I can send you a version off-list.

Cheers
\Heidi

> 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 at 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
>> >
>> >       [[alternative HTML version deleted]]
>> >
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>>
>>
>>
>