Question: oligo read.celfiles() error
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5.8 years ago by
Guest User12k
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I'm having trouble reading in my raw cel files and am unable to interpret the error message. Please see my error and code below. Last time I had to add varmetadata() info. and it worked, but that doesn't see to help in this case. Any suggestions will be appreciated. Thanks. Error: > OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, verbose=T) Platform design info loaded. Reading in : A1.CEL Reading in : A2.CEL Reading in : A3.CEL Reading in : A4.CEL Reading in : A5.CEL Reading in : B1.CEL Reading in : B2.CEL Reading in : B3.CEL Reading in : B4.CEL Reading in : B5.CEL Reading in : C1.CEL Reading in : C2.CEL Reading in : C3.CEL Reading in : C4.CEL Reading in : C5.CEL Reading in : D1.CEL Reading in : D2.CEL Reading in : D3.CEL Reading in : D4.CEL Reading in : D5.CEL Reading in : E1.CEL Reading in : E2.CEL Reading in : E3.CEL Reading in : E4.CEL Reading in : E5.CEL Reading in : F1.CEL Reading in : F2.CEL Reading in : F3.CEL Reading in : F4.CEL Reading in : F5.CEL Error in validObject(out) : invalid class ???GeneFeatureSet??? object: NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see ?"channelNames<-,NChannelSet,character-method" All code: rm(list=ls()) setwd("/Users/kasojima/Documents/Projects/Project_442/data/cel_files") #workdir="/Users/kasojima/Documents/Projects/Project_421" # resultsdir="/Users/kasojima/Documents/Projects/Project-421/R_Analysis" #Load Libraries library(oligo); #Set working directory to drive where cel files are #Read Affy cel files celfiles = list.files(path = ".", pattern = ".CEL$", all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE); #write("treatment", file = "covdesc.txt", append = FALSE, sep = "\t"); write(celfiles, file = "covdesc.txt",append = TRUE, sep = "\t"); #Create Affybatch #exp.data <- read.affy(covdesc="covdesc.txt"); #HTML file with other QC metrics?? ###Before running arrayQualityMetrics, you can modify the covdesc file to add sample information, e.g. time, cell type, treatment, etc. #import cel files using oligo pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="FileNa me" ,sep="\t") celFiles <- list.celfiles() x <- varMetadata(pd) x <- data.frame(x, channel = "_ALL_") varMetadata(pd) <- x OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, verbose=T) #MUST DETACH ALL AFFY PACKAGES AND ARRAYQUALITYMETRICS() IN ORDER FOR RMA TO WORK ON OLIGO OBJECTS!!** OligoNorm = rma(OligoRaw, target="core") #load libraries library (arrayQualityMetrics); library(affyPLM); #pData(exp.data) #Note column names in qcdef file and element in intgroup should match exactly #arrayQualityMetrics(expressionset = exp.data, intgroup = "Group", outdir = "QC", force =TRUE, do.logtransform = TRUE); arrayQualityMetrics(expressionset = OligoRaw, intgroup="group",outdir = "QC2", force =TRUE, do.logtransform = TRUE); -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 pd.hugene.2.0.st_3.8.0 RSQLite_0.11.4 [4] DBI_0.2-7 oligo_1.26.0 Biobase_2.22.0 [7] oligoClasses_1.24.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.0 affyio_1.30.0 Biostrings_2.30.1 [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 [7] foreach_1.4.1 GenomicRanges_1.14.4 IRanges_1.20.6 [10] iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 [13] stats4_3.0.2 tools_3.0.2 XVector_0.2.0 [16] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
affy oligo arrayqualitymetrics a4 • 1.8k views
ADD COMMENTlink modified 5.8 years ago by Kasoji, Manjula NIH/NCI [C]120 • written 5.8 years ago by Guest User12k
Answer: oligo read.celfiles() error
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gravatar for Kasoji, Manjula NIH/NCI [C]
5.8 years ago by
Found the answer from a previous post: Try adding your AnnotatedDataFrame after creating the ExpressionFeatureSet: dat <- read.celfiles(list.celfiles()) phenoData(dat) <- pd My apologies for the redundant post. Thanks. On 1/14/14 3:45PM, "Guest [guest]" <guest at="" bioconductor.org=""> wrote: > >I'm having trouble reading in my raw cel files and am unable to interpret >the error message. Please see my error and code below. Last time I had to >add varmetadata() info. and it worked, but that doesn't see to help in >this case. Any suggestions will be appreciated. > >Thanks. > >Error: > >> OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, >>verbose=T) >Platform design info loaded. >Reading in : A1.CEL >Reading in : A2.CEL >Reading in : A3.CEL >Reading in : A4.CEL >Reading in : A5.CEL >Reading in : B1.CEL >Reading in : B2.CEL >Reading in : B3.CEL >Reading in : B4.CEL >Reading in : B5.CEL >Reading in : C1.CEL >Reading in : C2.CEL >Reading in : C3.CEL >Reading in : C4.CEL >Reading in : C5.CEL >Reading in : D1.CEL >Reading in : D2.CEL >Reading in : D3.CEL >Reading in : D4.CEL >Reading in : D5.CEL >Reading in : E1.CEL >Reading in : E2.CEL >Reading in : E3.CEL >Reading in : E4.CEL >Reading in : E5.CEL >Reading in : F1.CEL >Reading in : F2.CEL >Reading in : F3.CEL >Reading in : F4.CEL >Reading in : F5.CEL >Error in validObject(out) : invalid class ?GeneFeatureSet? object: > NChannelSet levels(varMetadata(object)$channel) / >assayDataElementNames() > mismatch; see ?"channelNames<-,NChannelSet,character-method" > >All code: >rm(list=ls()) >setwd("/Users/kasojima/Documents/Projects/Project_442/data/cel_files" ) > >#workdir="/Users/kasojima/Documents/Projects/Project_421" ># resultsdir="/Users/kasojima/Documents/Projects/Project-421/R_Analysis" > >#Load Libraries >library(oligo); > >#Set working directory to drive where cel files are >#Read Affy cel files > >celfiles = list.files(path = ".", pattern = ".CEL$", all.files = FALSE, >full.names = FALSE, recursive = FALSE, ignore.case = FALSE); > >#write("treatment", file = "covdesc.txt", append = FALSE, sep = "\t"); > >write(celfiles, file = "covdesc.txt",append = TRUE, sep = "\t"); > >#Create Affybatch >#exp.data <- read.affy(covdesc="covdesc.txt"); >#HTML file with other QC metrics >###Before running arrayQualityMetrics, you can modify the covdesc file to >add sample information, e.g. time, cell type, treatment, etc. > >#import cel files using oligo > >pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="FileN ame" >,sep="\t") > >celFiles <- list.celfiles() >x <- varMetadata(pd) >x <- data.frame(x, channel = "_ALL_") >varMetadata(pd) <- x >OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, >verbose=T) > >#MUST DETACH ALL AFFY PACKAGES AND ARRAYQUALITYMETRICS() IN ORDER FOR RMA >TO WORK ON OLIGO OBJECTS!!** >OligoNorm = rma(OligoRaw, target="core") > >#load libraries >library (arrayQualityMetrics); >library(affyPLM); > >#pData(exp.data) > >#Note column names in qcdef file and element in intgroup should match >exactly >#arrayQualityMetrics(expressionset = exp.data, intgroup = "Group", outdir >= "QC", force =TRUE, do.logtransform = TRUE); >arrayQualityMetrics(expressionset = OligoRaw, intgroup="group",outdir = >"QC2", force =TRUE, do.logtransform = TRUE); > > > > -- output of sessionInfo(): > >> sessionInfo() >R version 3.0.2 (2013-09-25) >Platform: x86_64-apple-darwin10.8.0 (64-bit) > >locale: >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] parallel stats graphics grDevices utils datasets methods >base > >other attached packages: >[1] BiocInstaller_1.12.0 pd.hugene.2.0.st_3.8.0 RSQLite_0.11.4 >[4] DBI_0.2-7 oligo_1.26.0 Biobase_2.22.0 >[7] oligoClasses_1.24.0 BiocGenerics_0.8.0 > >loaded via a namespace (and not attached): > [1] affxparser_1.34.0 affyio_1.30.0 Biostrings_2.30.1 > [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 > [7] foreach_1.4.1 GenomicRanges_1.14.4 IRanges_1.20.6 >[10] iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 >[13] stats4_3.0.2 tools_3.0.2 XVector_0.2.0 >[16] zlibbioc_1.8.0 > > >-- >Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 5.8 years ago by Kasoji, Manjula NIH/NCI [C]120
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