The qpcR Package - NexTag Supports Open Source Initiatives

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10 efficiencyValueA list with the following components:effresVarAICcAICRsqcpD1cpD2cpEcpRfluoinitcfthe PCR efficiency.the residual variance.the bias-corrected Akaike Information Criterion.the Akaike Information Criterion.the R-square value.the first derivative maximum (point of inflection in ’l4’ or ’b4’ models, can beused for defining the threshold cycle).the second derivative maximum (turning point of cpD1, more often used fordefining the threshold cycle).the PCR cycle with the highest efficiency, if "maxE" method is chosen.the PCR cycle within the exponential region calculated as under ’Details’, if"expR" method is chosen.the raw fluorescence value at the point defined by type.the initial template fluorescence, i.e. F(0), calculated as under ’Details’.the conversion factor between raw fluorescence and template amount, if the latteris defined.NoteThree parameter models (’b3’ or ’l3’) do not work very well in calculating the PCR efficiency. Itis advisable not to take too many cycles of the plateau phase prior to fitting the model as this has astrong effect on the validity of the efficiency estimates.Author(s)Andrej-Nikolai Spiess & Christian RitzReferencesWeihong Liu and David A. Saint (2002) Validation of a quantitative method for real time PCRkinetics, BBRC, 294, 347 - 353.Examples## Fitting initial modelm1
evidence 11efficiency(m2, type = "maxE", shift = 1)##using the exponential regionefficiency(m2, type = "expR")## using threshold value (15.32) from PCR softwareefficiency(m2, type = 15.32)## using the first 30 cycles and a template amountm3
Page 1 and 2: The qpcR PackageFebruary 16, 2008Ty
Page 3 and 4: RMSE 3Author(s)Andrej-Nikolai Spies
Page 5 and 6: calib 5DetailsThe real-time PCR was
Page 7 and 8: confband 7Examples###define dilutio
Page 9: efficiency 9Examplesm
Page 13 and 14: expfit 13expfitCalculation of PCR e
Page 15 and 16: mchoice 15ValueA list with the foll
Page 17 and 18: pcrGOF 17DetailsValueFor a more det
Page 19 and 20: pcrfit 19DetailsValueThe qPCR raw d
Page 21 and 22: pcropt1 21Argumentsfilesepheaderquo
Page 23 and 24: pcrplot 23pcrplotPlotting PCR data
Page 25 and 26: qpcR 25Usagepcrpred(object, newdata
Page 27 and 28: epform 27confband qPCR data from Ru
Page 29 and 30: eps2 29Examplesdata(reps)### on sin
Page 31 and 32: esVar 31resVarResidual variance of
Page 33 and 34: sliwin 33DetailsValueTo avoid fits
Page 35: INDEX 35mchoice, 15modlist, 16multd

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