NormqPCR and ReadqPCR
1
0
Entering edit mode
Pepijn Kooij ▴ 10
@pepijn-kooij-5103
Last seen 8.4 years ago
Dear all My name is Pepijn Kooij, PhD student at the Centre for Social Evolution, Copenhagen University. I was grateful to find the ReadqPCR and NormqPCR packages to analyze my rt-qPCR data. I managed to use both packages, loading in my data and normalizing it. In the end using the deltaDeltaCt() function I am able to retrieve the table with all the data I need. My question now is, is there a way or package to go further from this? As in, I am interested to see which of the genes have a foldchange above a threshhold of 1, is there a way to see that? And, is it possible to plot the 2^∆∆Ct values in a bargraph with SD's or SE's? I hope you can help me out with this, Best regards Pepijn Kooij _______________________________________ Pepijn Kooij, PhD student Centre for Social Evolution, Department of Biology University of Copenhagen Universitetsparken 15, bygning 12 2100 Copenhagen Ø Denmark Tel: (+45) 35 32 13 41 Email: pkooij@bio.ku.dk CSE website: http://www.bi.ku.dk/cse [[alternative HTML version deleted]]
GO ReadqPCR NormqPCR GO ReadqPCR NormqPCR • 911 views
ADD COMMENT
0
Entering edit mode
james perkins ▴ 300
@james-perkins-2675
Last seen 8.4 years ago
HI Pepijn Thanks for your interest. >My question now is, is there a way or package to go further from this? As in, I am interested to see which of the genes have a foldchange above a threshhold of 1, is there a way to see that? By a "foldchange threshold of 1", do you mean a doubling or halving? i.e. |logFC | > 1? If so you can find everything in your ddCt output data.frame that meets this criteria and look at only these genes. ddCtRes[abs(log2(as.numeric(as.vector(ddCtRes$`2^-ddCt`)))) > 1,] For the gene IDs alone this will work: ddCtRes[abs(log2(as.numeric(as.vector(ddCtRes$`2^-ddCt`)))) > 1,"ID"] This is assuming you have done something with the undetermined values, if you have "+"s and "-"s for your 2^ddCt values it gets a bit more involved. >And, is it possible to plot the 2^∆∆Ct values in a bargraph with SD's or SE's? I hope you can help me out with this, It is possible, you could use something like barplot2 from gplots and plot the min 2^-ddCt.min and max values 2^-ddCt.max as upper and lower confidence intevals. The min and max values are calculated along the lines of http://www.ncbi.nlm.nih.gov/pubmed/11846609, and the error bars will be assymetric if you plot the x axis in non-log space, since the Ct values from which SD worked out on arithmetic scale but then gets 2^ddCT+/-SD. arguments to barplot2 something like: plot.ci=TRUE, ci.l=MIN2^DDCTS, ci.u=MIN2^DDCTS, Hope this helps, let me know if you have any issues with the plotting, and if you want to send me a more concrete example I can give some more focused code. Cheers, Jim On 8 February 2012 16:32, Pepijn Kooij <pkooij@bio.ku.dk> wrote: > Dear all > > My name is Pepijn Kooij, PhD student at the Centre for Social Evolution, > Copenhagen University. > I was grateful to find the ReadqPCR and NormqPCR packages to analyze my > rt-qPCR data. I managed to use both packages, loading in my data and > normalizing it. In the end using the deltaDeltaCt() function I am able to > retrieve the table with all the data I need. > My question now is, is there a way or package to go further from this? As > in, I am interested to see which of the genes have a foldchange above a > threshhold of 1, is there a way to see that? > And, is it possible to plot the 2^∆∆Ct values in a bargraph with SD's or > SE's? > I hope you can help me out with this, > > Best regards > Pepijn Kooij > _______________________________________ > Pepijn Kooij, PhD student > Centre for Social Evolution, Department of Biology > University of Copenhagen > Universitetsparken 15, bygning 12 > 2100 Copenhagen Ø > Denmark > > Tel: (+45) 35 32 13 41 > Email: pkooij@bio.ku.dk > CSE website: http://www.bi.ku.dk/cse > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 620 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6