oligo read.celfiles() error
1
0
Entering edit mode
Guest User ★ 12k
@guest-user-4897
Last seen 6.8 years ago
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 affy oligo arrayQualityMetrics a4 • 2.1k views
ADD COMMENT
0
Entering edit mode
@kasoji-manjula-nihnci-c-5538
Last seen 6.8 years ago
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.

Login before adding your answer.

Traffic: 355 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6