[BioC] oligo read celfile

[Benilton Carvalho]

the name of the object where you read your files into is:

affyGenesFS

and not

affyGeneFS

b

On 24 May 2011 23:32, YBao <yb8d at virginia.edu> wrote:
> 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
>
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