Hello, I have qPCR data that does not have Well and Plate info to populate qPCRBatch object. As your vignette points, out, I am trying to create an eSet object: > frame<-read.delim("dreamy.csv", skip=2, sep="\t", colClasses="character") > n=30 > head(frame) Actin_022.Triton.X.control.hskg.20.59.1 1 Actin_022\tTriton-X\tcontrol\thskg\t20.00\t2 2 Actin_022\tTriton-X\tcontrol\thskg\t22.96\t3 3 Actin_122\tTriton-X\tcontrol\thskg\t20.95\t1 4 Actin_122\tTriton-X\tcontrol\thskg\t20.86\t2 5 Actin_122\tTriton-X\tcontrol\thskg\t20.96\t3 6 Actin_322\tTriton-X\tcontrol\thskg\t20.97\t1 ## new("eSet", class=matrix) of Ct values > mat=matrix(as.numeric(frame$Ct), ncol=1, nrow=30, byrow=FALSE) > summary(mat) V1 V2 V3 V4 V5 Min. : NA Min. : NA Min. : NA Min. : NA Min. : NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA Median : NA Median : NA Median : NA Median : NA Median : NA Mean :NaN Mean :NaN Mean :NaN Mean :NaN Mean :NaN 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA Max. : NA Max. : NA Max. : NA Max. : NA Max. : NA NA's :30 NA's :30 NA's :30 NA's :30 NA's :30 ## use eSet formatting new("ExpressionSet", phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), exprs = new("matrix")) ... > rawdog<-new("qPCRset", exprs=mat, phenoData=as(data.frame(frame$featureType, rep(c("control", "target"), each=15), frame$featureClass, rep(c("hkgs, "jasmonic pathway", each=15), featureData=as(data.frame(frame$featureNames, rep(c("Gene", 1:n, sep="\t"))))) ##But get undetermined error. Error: unexpected symbol in "rawdog<-new("qPCRset", exprs=mat, phenoData=as(data.frame(frame$featureType, rep(c("control", "target"), each=15), as(data.frame(frame$featureClass, rep(c("hkgs, "jasmonic" ##Also tried to use methods: "AnnotatedDataFrameFrom", (coerse using: phenoData=(phenodata)), (AnnotatedDataFrame"), rbind() <-get error message that matrix must be of AssayData type ##tried adding paretheses to ("frame$columnName") > rawdog<-new("qPCRset", exprs=mat,phenoData=as(data.frame(frame$featureType), rep(c("control", "target"), each=15), (frame$featureClass, rep(c("hkgs, "jasmonic pathway", each=15), featureData=as(data.frame(frame$featureNames, rep(c("Gene", 1:n, sep="\t")))) Error: unexpected ',' in "rawdog<-new("qPCRset", exprs=mat,phenoData=as(data.frame(frame$featureType), rep(c("control", "target"), each=15), (frame$featureClass," ##Mixed from HTqPCR vinette and R scripts > raw=new("qPCRset", exprs=mat, phenoData=AnnotatedDataFrame(array(frame$featureNames, frame$SampleName),featureData=AnnotatedDataFrame(frame$featureType, frame$featureCategory))) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "AnnotatedDataFrame", for signature "NULL", "missing" >Dreamy.csv Sample Detector featureNames sampleNames featureType featureClass Ct replicateType Actin_022 Triton-X control hskg 20.59 1 Actin_022 Triton-X control hskg 20.00 2 Actin_022 Triton-X control hskg 22.96 3 Actin_122 Triton-X control hskg 20.95 1 Actin_122 Triton-X control hskg 20.86 2 Actin_122 Triton-X control hskg 20.96 3 Actin_322 Triton-X control hskg 20.97 1 Actin_322 Triton-X control hskg 21.18 2 Actin_322 Triton-X control hskg 21.81 3 Actin_722 Triton-X control hskg 21.14 1 Actin_722 Triton-X control hskg 20.85 2 Actin_722 Triton-X control hskg 21.78 3 Actin_1422 Triton-X control hskg 21.54 1 Actin_1422 Triton-X control hskg 21.11 2 Actin_1422 Triton-X control hskg 22.45 3 Lox22_022 Triton-X target jasmonic pathway 23.93 1 Lox22_022 Triton-X target jasmonic pathway 23.36 2 Lox22_022 Triton-X target jasmonic pathway 23.52 3 Lox22_122 Triton-X target jasmonic pathway 24.82 1 Lox22_122 Triton-X target jasmonic pathway 24.71 2 Lox22_122 Triton-X target jasmonic pathway 25.61 3 Once I figure out the eSet formatting, I Would also like to add a column to phenoData: [[replicateType]] to tell R that I have replicates. I have simulated the data above, however, I have N=3 samples (untreated control, negative control, and treated) each having 2 technical replicates Actin_022 is paired with Lox22_022, each having 3 biological replicates, respectively. If possible, could you offer help on rawdog<-new(eSet, "AnnotatedDataFrameS") Best Regards, Franklin -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] NormqPCR_1.4.0 ReadqPCR_1.4.0 affy_1.36.1 BiocInstaller_1.8.3 HTqPCR_1.12.0 limma_3.14.0 [7] RColorBrewer_1.0-5 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 gdata_2.12.0 gplots_2.11.0 gtools_2.7.0 preprocessCore_1.20.0 stats4_2.15.1 [7] tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Franklin, First, sending the same exact email under two different threads is not considered good form. On 2/24/2013 4:34 PM, Franklin Johnson [guest] wrote: > Hello, > > I have qPCR data that does not have Well and Plate info to populate qPCRBatch object. As your vignette points, out, I am trying to create an eSet object: > >> frame<-read.delim("dreamy.csv", skip=2, sep="\t", colClasses="character") >> n=30 >> head(frame) > Actin_022.Triton.X.control.hskg.20.59.1 > 1 Actin_022\tTriton-X\tcontrol\thskg\t20.00\t2 > 2 Actin_022\tTriton-X\tcontrol\thskg\t22.96\t3 > 3 Actin_122\tTriton-X\tcontrol\thskg\t20.95\t1 > 4 Actin_122\tTriton-X\tcontrol\thskg\t20.86\t2 > 5 Actin_122\tTriton-X\tcontrol\thskg\t20.96\t3 > 6 Actin_322\tTriton-X\tcontrol\thskg\t20.97\t1 Is this really what you expect to see? Do you not find it odd that you have a single column, with everything separated by a \t? Additionally, are you aware that 'csv' stands for comma-separated values? I would recommend getting this first step sorted out prior to going on. Best, Jim > > ## new("eSet", class=matrix) of Ct values >> mat=matrix(as.numeric(frame$Ct), ncol=1, nrow=30, byrow=FALSE) >> summary(mat) > V1 V2 V3 V4 V5 > Min. : NA Min. : NA Min. : NA Min. : NA Min. : NA > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA > Median : NA Median : NA Median : NA Median : NA Median : NA > Mean :NaN Mean :NaN Mean :NaN Mean :NaN Mean :NaN > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA > Max. : NA Max. : NA Max. : NA Max. : NA Max. : NA > NA's :30 NA's :30 NA's :30 NA's :30 NA's :30 > > ## use eSet formatting > new("ExpressionSet", phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), > experimentData = new("MIAME"), annotation = character(0), exprs = new("matrix")) > ... >> rawdog<-new("qPCRset", exprs=mat, phenoData=as(data.frame(frame$featureType, rep(c("control", "target"), each=15), > frame$featureClass, rep(c("hkgs, "jasmonic pathway", each=15), > featureData=as(data.frame(frame$featureNames, rep(c("Gene", 1:n, sep="\t"))))) > ##But get undetermined error. > Error: unexpected symbol in "rawdog<-new("qPCRset", exprs=mat, phenoData=as(data.frame(frame$featureType, rep(c("control", "target"), each=15), > as(data.frame(frame$featureClass, rep(c("hkgs, "jasmonic" > > ##Also tried to use methods: "AnnotatedDataFrameFrom", (coerse using: phenoData=(phenodata)), (AnnotatedDataFrame"), > rbind()<-get error message that matrix must be of AssayData type > > ##tried adding paretheses to ("frame$columnName") >> rawdog<-new("qPCRset", exprs=mat,phenoData=as(data.frame(frame$featureType), rep(c("control", "target"), each=15), (frame$featureClass, rep(c("hkgs, "jasmonic pathway", each=15), featureData=as(data.frame(frame$featureNames, rep(c("Gene", 1:n, sep="\t")))) > Error: unexpected ',' in "rawdog<-new("qPCRset", exprs=mat,phenoData=as(data.frame(frame$featureType), rep(c("control", "target"), each=15), (frame$featureClass," > ##Mixed from HTqPCR vinette and R scripts >> raw=new("qPCRset", exprs=mat, phenoData=AnnotatedDataFrame(array(frame$featureNames, frame$SampleName),featureData=AnnotatedDataFrame(frame$featureType, > frame$featureCategory))) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "AnnotatedDataFrame", for signature "NULL", "missing" > >> Dreamy.csv > Sample Detector > featureNames sampleNames featureType featureClass Ct replicateType > Actin_022 Triton-X control hskg 20.59 1 > Actin_022 Triton-X control hskg 20.00 2 > Actin_022 Triton-X control hskg 22.96 3 > Actin_122 Triton-X control hskg 20.95 1 > Actin_122 Triton-X control hskg 20.86 2 > Actin_122 Triton-X control hskg 20.96 3 > Actin_322 Triton-X control hskg 20.97 1 > Actin_322 Triton-X control hskg 21.18 2 > Actin_322 Triton-X control hskg 21.81 3 > Actin_722 Triton-X control hskg 21.14 1 > Actin_722 Triton-X control hskg 20.85 2 > Actin_722 Triton-X control hskg 21.78 3 > Actin_1422 Triton-X control hskg 21.54 1 > Actin_1422 Triton-X control hskg 21.11 2 > Actin_1422 Triton-X control hskg 22.45 3 > Lox22_022 Triton-X target jasmonic pathway 23.93 1 > Lox22_022 Triton-X target jasmonic pathway 23.36 2 > Lox22_022 Triton-X target jasmonic pathway 23.52 3 > Lox22_122 Triton-X target jasmonic pathway 24.82 1 > Lox22_122 Triton-X target jasmonic pathway 24.71 2 > Lox22_122 Triton-X target jasmonic pathway 25.61 3 > > Once I figure out the eSet formatting, I Would also like to add a column to phenoData: [[replicateType]] to tell R that I have replicates. I have simulated the data above, however, I have N=3 samples (untreated control, negative control, and treated) each having 2 technical replicates Actin_022 is paired with Lox22_022, each having 3 biological replicates, respectively. > > If possible, could you offer help on rawdog<-new(eSet, "AnnotatedDataFrameS") > > Best Regards, > > Franklin > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] NormqPCR_1.4.0 ReadqPCR_1.4.0 affy_1.36.1 BiocInstaller_1.8.3 HTqPCR_1.12.0 limma_3.14.0 > [7] RColorBrewer_1.0-5 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 gdata_2.12.0 gplots_2.11.0 gtools_2.7.0 preprocessCore_1.20.0 stats4_2.15.1 > [7] tools_2.15.1 zlibbioc_1.4.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Dear James, Thanks for your reply. Very useful information, indeed. Much appreciation. Now I can import into NormqPCR and HTqPCR. I'm having some issues, but, I'm gonna try and work them out. I'm sure you'll hear from me again. Regards, Franklin -- output of sessionInfo(): N/A -- Sent via the guest posting facility at bioconductor.org.