[BioC] reading in data in ReadqPCR
James W. MacDonald
jmacdon at uw.edu
Mon Feb 25 15:10:30 CET 2013
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
More information about the Bioconductor
mailing list