[BioC] PCR efficiency correction with HTqPCR

[Heidi Dvinge]

Hi Max,

> Hi,
>
> I'd like to know if anyone has managed to use HTqPCR analysis for real
> time qPCR analysis, with deltaCt normalisation, but also incorporating a
> PCR efficiency correction? How would I go about doing this?
>
Currently there's no default way of doing this in HTqPCR, but depending on
what sort of information you have, it should be posisible. Does your data
include a calibration curve that you first need to calculate the PCR
efficiency from? Or do you have this value somehow from the qPCR software?

> My second question concerns normalisation using deltaCt method. I have
> noticed that when there is a missing value as in Ct value missing, it
> fails to determine mean.  Not sure what to do here.
>
What sort of values (text?) in your input file results in NAs? Usually
these should be replaced with e.g. a Ct value of 40 when reading in the
data, so I'm curious as to why that doesn't happen for your input.

I'll add a check for this in deltaCt. In the meantime, you can replace all
your NAs saying:

exprs(q)[is.na(exprs(q))] <- 40

where q is your qPCRset object.

HTH
\Heidi
> Thanks in advance.
>
> Kind regards
> Max
>
> Maxy Mariasegaram| Reserach Fellow | Australian Prostate Cancer Research
> Centre| Level 1, Building 33 | Princess Alexandra Hospital | 199 Ipswich
> Road, Brisbane QLD 4102 Australia | t: 07 3176 3073| f: 07 3176 7440 | e:
> mariaseg at qut.edu.au
>
>
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