[BioC] HTqPCR - how to read data file with multiple samples

[Heidi Dvinge]

Hello Adam,

just a quick email to let you know that I've implemented your  
suggested changes in HTqPCR. This includes e.g. a getCt() and history 
() funciton, along with adjusted p-values for the t-test.

These functions are available in v. 1.1.2 that should be available  
from the BioC devel repository within the next few days.

Cheers
\Heidi

On 12 Jan 2010, at 17:30, Adam Kiezun wrote:

> Great,
> Thanks Heidi. This worked nicely.
>
>> Can you give me a bit more details about how these files were  
>> generated?
>> Is it a standard TLDA card from ABI (with 381 features or have 3  
>> genes
>> automatically been excluded)? Are the cards analysed in batch  
>> somehow on
>> the SDS software, or are they processed individually and then just
>> exported to a text file together?
>
> I actually don't know. I'm analysing the data for someone else who did
> the experiment. The cards contain microRNAs, not protein-coding genes.
> There are 2 plates actually, one with 381 and the other with 216
> miRNAs. We got the files from AB in the format I showed you - I don't
> know how they exported it.
>
> One useful feature for the HTqPCR package would be to include adjusted
> p-values (method could be passed as a parameter eg "FDR"), and fold
> changes. It's something everyone needs anyway. Right now, I called
> p.adjust and 2^(-ddCt) myself and added those as a column in the
> result table. But it would be nicer to have this work automagically.
>
> Another convenience would be to have the qPCR object remember what
> normalizations and filterings were done on it (like the objects in the
> lumi package). Right now,  I store this in the name of the variable
> (eg raw.cat.filt.qnorm) but that's suboptimal.
>
> It should be more intuitive to access Ct values from the qPCR object.
> Right now, it's something like exprs(object). How about simply
> ctValues(object) or something?
>
> A nitpick: it would be nice to have the documentation contain the code
> to create all figures presented (missing for Figures 6, 7)
>
> All in all, it's a great package. Thanks for your help and I look
> forward to future improvements.
> ./adam