[BioC] HTqPCR package data layout - how flexible is it?

Ruben Alvarez [guest] guest at bioconductor.org
Thu Jun 12 15:03:22 CEST 2014

Dear Heidi (and all),

Thank you very much for your work on this package. I found the vignettes and the info supplied excellent!

My question is about the featureData layout. 

My experiment is as follows. I have 96-well qPCR plates to read on a LightCycler, and for my samples I think the best arrangement is:

- one gene (primer pair) per plate (with one or two plates for endogenous controls). We are not completely sure on how many genes we will need to test, and with this modular design we can add more if needed.

- one inter-plate calibrator (technical replicates of the same cDNA in each plate, to allow for inter-plate normalisation).

- two treatments ('control' and 'treatment')

- all samples (cDNA's, including biological replicates) are present in each of the plates.

- three biological replicates (I have a fourth one that I would use if there is too much difference between them).

- two technical replicates (I have space constraints and my repeatability seems good).

The questions are:
- changeCtLayout will allow me to prepare the cards (96-well plates) for multiple samples, but how can I repeat that layout for each card? My understanding is that a different card implies a different sample with the standard HT-qPCR layout, but in my case each card would have the same samples but a different featureName.

- in the event that I need to add a fourth biological replicate, how straightforward would it be to add normalised data to the initial (3-bioreps) normalised data?

I think I am in the low end of intermediate R knowledge (and sometimes I see myself as naive...), and very much appreciate the help!


 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

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