Question: Opening Data for NormqPCR (readqPCR)
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4.9 years ago by
Guest User12k
Guest User12k wrote:
Dear all, I'm a phD student in Center of Cancerology of Toulouse France. I'm a new R user, and I would like to use the package "NormqPCR" for the functions geNorm and Normfinder. I don't have raw data file, I have a file which I can modify with sample names, gene names and Ct values where I don't have replicates because I was using Fluidigm method for amplification. How to do to use the function read.qPCR, how to configure my tab with Ct values to allow R to load my data? Best regards Camille -- output of sessionInfo(): read.qPCR -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 4.9 years ago by James Perkins60 • written 4.9 years ago by Guest User12k
Answer: Opening Data for NormqPCR (readqPCR)
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4.9 years ago by
Spain
James Perkins60 wrote:
Hi Camille There are some examples in the vignette for the package. You can see an example file by using: path <- system.file("exData", package = "ReadqPCR") qPCR.example <- file.path(path, "qPCR.example.txt") More details are given in section 3, page 7 of the vignette, of the different columns needed. It will work without technical replicates, as long as the gene names are distinct. Presumably you have biological replicates? Jim On 14 June 2014 14:56, Camille [guest] <guest@bioconductor.org> wrote: > Dear all, > > I'm a phD student in Center of Cancerology of Toulouse France. I'm a new R > user, and I would like to use the package "NormqPCR" for the functions > geNorm and Normfinder. > I don't have raw data file, I have a file which I can modify > with sample names, gene names and Ct values where I don't have replicates > because I was using Fluidigm method for amplification. > How to do to use the function read.qPCR, how to configure my tab with Ct > values to allow R to load my data? > Best regards > > Camille > > -- output of sessionInfo(): > > read.qPCR > > -- > Sent via the guest posting facility at bioconductor.org. > > -- James R Perkins PhD Marie Curie Post-Doctoral Researcher Research Laboratory, Allergy Unit University Hospital of Malaga-IBIMA 29009 Malaga, Spain [[alternative HTML version deleted]]
ADD COMMENTlink written 4.9 years ago by James Perkins60
Hello James, Thank you for your answer. I manage to open my file and runnung Genorm with the following script: (I have a text file with genes in the 1st five columns and groups identifiers in the 6th one) donnees <- as.matrix(read.table("housekeeping_genes_ALK.txt", header=TRUE, sep="\t",row.names=1, as.is=TRUE)) hkgs<-c("RPL0","GAPDH","MLN51","X28S","X18S") hkgsGenorm <-selectHKs(donnees[,-6], method = "geNorm", minNrHKs = 2, log = TRUE, Symbols=hkgs ,trace = TRUE, na.rm = TRUE) I think Genorm is working with this script, however I'm not able to run NormFinder correctly. Camille 2014-06-16 11:49 GMT+02:00 James Perkins <jimrperkins@gmail.com>: > Hi Camille > > There are some examples in the vignette for the package. > > You can see an example file by using: > > path <- system.file("exData", package = "ReadqPCR") > qPCR.example <- file.path(path, "qPCR.example.txt") > > More details are given in section 3, page 7 of the vignette, of the different columns needed. > > > It will work without technical replicates, as long as the gene names are distinct. Presumably you have biological replicates? > > > Jim > > > > > > > > On 14 June 2014 14:56, Camille [guest] <guest@bioconductor.org> wrote: > >> Dear all, >> >> I'm a phD student in Center of Cancerology of Toulouse France. I'm a new >> R user, and I would like to use the package "NormqPCR" for the functions >> geNorm and Normfinder. >> I don't have raw data file, I have a file which I can modify >> with sample names, gene names and Ct values where I don't have replicates >> because I was using Fluidigm method for amplification. >> How to do to use the function read.qPCR, how to configure my tab with Ct >> values to allow R to load my data? >> Best regards >> >> Camille >> >> -- output of sessionInfo(): >> >> read.qPCR >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> > > > -- > James R Perkins PhD > Marie Curie Post-Doctoral Researcher > Research Laboratory, Allergy Unit > University Hospital of Malaga-IBIMA > 29009 Malaga, Spain > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.9 years ago by camille daugrois10
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