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
>
>
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