[BioC] oligo read.celfiles() error

[Guest [guest]]

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="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       


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