[BioC] oligo read celfile

[YBao]

Dear R-B Experts,

I ran into a problem using the oligo package to analyze mgst arrays.
It seems the read.celfiles() did not actually read in the new data but
instead keeping the old data read in previously.
> library(oligo)
> library(pd.mogene.1.0.st.v1)
> geneCELs <- list.celfiles("/Data_Analysis/Yu2011_183mgst", full.names = TRUE)
> affyGenesFS <- read.celfiles (geneCELs)
Platform design info loaded.
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT1_(MoGene-1_0-st-v1).CEL
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT2_(MoGene-1_0-st-v1).CEL
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT3_(MoGene-1_0-st-v1).CEL
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT1_(MoGene-1_0-st-v1).CEL
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT2_(MoGene-1_0-st-v1).CEL
Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT3_(MoGene-1_0-st-v1).CEL
> affyGeneFS
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 33 samples
  element names: exprs
protocolData
  rowNames: TisMap_Brain_01_v1_WTGene1.CEL
TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL
(33 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: TisMap_Brain_01_v1_WTGene1.CEL
TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL
(33 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hugene.1.0.st.v1

This remains the same even after I reload all the packages again and
started fresh. Any help would be greatly appreciated.

Here is the session info:
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] pd.hugene.1.0.st.v1_3.0.2 oligoData_1.0.0
pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0
oligoClasses_1.12.2
 [6] RColorBrewer_1.0-2        geneplotter_1.28.0
annotate_1.28.1           annaffy_1.22.0            KEGG.db_2.4.5
[11] GO.db_2.4.5               RSQLite_0.9-3             DBI_0.2-5
            AnnotationDbi_1.12.0      affyQCReport_1.28.1
[16] lattice_0.19-13           simpleaffy_2.26.1
genefilter_1.32.0         limma_3.6.9               affyPLM_1.26.1
[21] preprocessCore_1.12.0     gcrma_2.22.0
affydata_1.11.11          affy_1.28.0               Biobase_2.10.0
[26] R.utils_1.5.7             R.oo_1.7.4
R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] affxparser_1.22.1 affyio_1.18.0     Biostrings_2.18.4 grid_2.12.2
     IRanges_1.8.9     splines_2.12.2    survival_2.36-1
tools_2.12.2
[9] xtable_1.5-6

Best,

Yongde