Hi Andreia,

the Ct values for qPCRset objects can be subset like any standard R- 
object, i.e. using the [,] notation. samplesNames() just gives you  
the names of the individual samples. If you want to plot e.g. sample  
1 you can say:

plot(exprs(raw.cat)[,1], exprs(q.norm)[,1])

If you have for example 4 samples, you can plot them next to each  
other like in the vignette by changing some parameters in par().

par(mfrow=c(2,2), mar=c(2,2,2,1))
for (i in 1:4) {
	plot(exprs(raw.cat)[,i], exprs(q.norm)[,i])
}

If you mean with a different colour for each sample like in the  
vignette, then you can define a colour vector such as

my.col <- rep(brewer.pal(n.samples(raw.cat), "Spectral"), each=n.wells 
(raw.cat))
plot(exprs(raw.cat), exprs(q.norm), pch=20, col=my.col)

In the latest version of HTqPCR (1.1.2) the vignette includes a bit  
more about the raw versus normalised plots in figure 6, since I've  
had other requests for that.

HTH
\Heidi

On 20 Jan 2010, at 11:37, Andreia Fonseca wrote:

> Hi Heidi,
>
> sorry but I am back at HTqPCR again and I am trying to produce the  
> plots raw Ct versus normalized CT values. I am using the command
> plot(exprs(raw.cat)~exprs(q.norm))
>
> but I would like to plot it per sample, like in the manual, I saw  
> that sampleNames() function but I am not managing to understand how  
> to put it in the plot command. Can you tell me how you did it?
>
> Cheers
> Andreia
>
> On Tue, Jan 19, 2010 at 5:54 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:
> Hello Alberto,
>
> it's not in BioConductor, and I've never used it myself, but the  
> package qpcR might be able to do what you're after.  As far as I  
> remember it's on CRAN, but if not you can get it from http://www.dr- 
> spiess.de/qpcR.html
>
> Cheers
> \Heidi
>
>
>
> On 19 Jan 2010, at 11:09, Alberto Goldoni wrote:
>
> Dear all,
> there is a method to calculate the Ct value if i have the file.txt  
> with the fuolescence intensity like this one:
>
> Raw Data
>        Experiment - PIASTRA 1 ALL+CML (Run on LCS480 1.2.9.11)
>
>
>
>
> SamplePos       SampleName      Prog#   Seg#    Cycle#  Time     
> Temp    483-533
> A1      4200_ABL        2       2       1       420616  59.93   6.67
> A1      4200_ABL        2       2       2       529833  59.93   6.72
> A1      4200_ABL        2       2       3       639216  59.96   6.86
> A1      4200_ABL        2       2       4       748850  59.96   6.94
> A1      4200_ABL        2       2       5       858416  59.96   7.53
> A1      4200_ABL        2       2       6       967600  59.96   7.59
> A1      4200_ABL        2       2       7       1076816          
> 59.96   7.64
> A1      4200_ABL        2       2       8       1186033          
> 59.93   7.69
> A1      4200_ABL        2       2       9       1295616          
> 59.96   7.74
> A1      4200_ABL        2       2       10      1404816          
> 59.96   7.77
> A1      4200_ABL        2       2       11      1513816          
> 59.96   7.79
> A1      4200_ABL        2       2       12      1623000          
> 59.96   7.86
> A1      4200_ABL        2       2       13      1732650          
> 59.96   7.87
> A1      4200_ABL        2       2       14      1841800          
> 59.96   7.92
> A1      4200_ABL        2       2       15      1951033          
> 59.96   7.93
> A1      4200_ABL        2       2       16      2060000          
> 59.96   7.95
> A1      4200_ABL        2       2       17      2169216          
> 59.96   7.99
> A1      4200_ABL        2       2       18      2278233          
> 59.96   8
> A1      4200_ABL        2       2       19      2387216          
> 59.93   8
> A1      4200_ABL        2       2       20      2496433          
> 59.96   8.03
> A1      4200_ABL        2       2       21      2605616          
> 59.93   8.05
> A1      4200_ABL        2       2       22      2714816          
> 59.96   8.06
> A1      4200_ABL        2       2       23      2824016          
> 59.96   8.08
> A1      4200_ABL        2       2       24      2933183          
> 59.96   8.12
> A1      4200_ABL        2       2       25      3042433          
> 59.96   8.16
> A1      4200_ABL        2       2       26      3151633          
> 59.93   8.22
> A1      4200_ABL        2       2       27      3260833          
> 59.96   8.3
> A1      4200_ABL        2       2       28      3370016          
> 59.93   8.42
>
>
> -- 
> ----------------------------------------
> Alberto Goldoni, PhD
> IT Lan Manager
> Medical Genetics Unit
> S. Orsola-Malpighi Hospital
> Via Massarenti n.9, Pad 11
> 40100 Bologna, Italy
> ----------------------------------------
>
> <PIASTRA 1 ALL+CML.txt>_______________________________________________
>
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/ 
> gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/ 
> gmane.science.biology.informatics.conductor
>
>
>
> -- 
> --------------------------------------------
> Andreia J. Amaral
> Unidade de Imunologia Clínica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral@fm.ul.pt
>          andreia.fonseca@gmail.com


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