Question: problem with qPCR raw data
0
gravatar for Alberto Goldoni
9.8 years ago by
Alberto Goldoni60 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 ---------------------------------------- -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: PIASTRA 1 ALL+CML.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100119="" 61f36417="" attachment.txt="">
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ADD COMMENTlink modified 9.8 years ago by Heidi Dvinge2.0k • written 9.8 years ago by Alberto Goldoni60
Answer: problem with qPCR raw data
0
gravatar for Heidi Dvinge
9.8 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.8 years ago by Heidi Dvinge2.0k
Answer: problem with qPCR raw data
0
gravatar for Heidi Dvinge
9.8 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
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(exprsraw.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(exprsraw.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.samplesraw.cat), "Spectral"), each=n.wells raw.cat)) plot(exprsraw.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(exprsraw.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 ClĂ­nica > Instituto de Medicina Molecular > Universidade de Lisboa > email: andreiaamaral@fm.ul.pt > andreia.fonseca@gmail.com [[alternative HTML version deleted]]
ADD COMMENTlink written 9.8 years ago by Heidi Dvinge2.0k
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