[BioC] oligo read.celfiles() error

[Kasoji, Manjula (NIH/NCI) [C]]

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 ³GeneFeatureSet² 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="FileName"
>,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.