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? 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. 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@qut.edu.au [[alternative HTML version deleted]]

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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >