[BioC] create the expression set

[James W. MacDonald]

You don't need an ExpressionSet to analyze data using limma. You can 
instead use a matrix. See ?lmFit for more information.

Best,

Jim



On 6/26/2014 1:59 PM, guest [guest] wrote:
> Dear Users,
>
> I tried to create the ExpressionSet using the normalized microarray data.
>
>> normdata=read.csv("import_transpose_koho.csv", header=T, sep='t', stringsAsFactors =F)
>
> ##### read the pheno data
>> pheno=read.table("sampleInfo.csv", header=T,sep=',',skip=0,stringsAsFactors=F)
>> pd <- new("AnnotatedDataFrame", data = as.data.frame(pheno))
>> Dset<-new("ExpressionSet", exprs=normdata, phenoData=pd)
> Error in (function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘annotatedDataFrameFrom’ for signature ‘"data.frame"’
>
> I am quite new to this, maybe it isn't related to limma package. Does anyone know what's wrong with the dataframe?
>
> Thanks a lot for the help, I really appreciate it.
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> 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  grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] kohonen_2.0.14                           MASS_7.3-33                              class_7.3-10
>   [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 gdata_2.13.3                             limma_3.20.5
>   [7] methyAnalysis_1.6.0                      methylumi_2.10.0                         minfi_1.10.2
> [10] bumphunter_1.4.2                         locfit_1.5-9.1                           iterators_1.0.7
> [13] foreach_1.4.2                            lattice_0.20-29                          matrixStats_0.10.0
> [16] ggplot2_1.0.0                            reshape2_1.4                             scales_0.2.4
> [19] FDb.InfiniumMethylation.hg19_2.0.10      BSgenome.Hsapiens.UCSC.hg19_1.3.99       BSgenome_1.32.0
> [22] Biostrings_2.32.0                        XVector_0.4.0                            GenomicFeatures_1.16.2
> [25] org.Hs.eg.db_2.14.0                      RSQLite_0.11.4                           DBI_0.2-7
> [28] AnnotationDbi_1.26.0                     Biobase_2.24.0                           GenomicRanges_1.16.3
> [31] GenomeInfoDb_1.0.2                       IRanges_1.22.9                           BiocGenerics_0.10.0
> [34] BiocInstaller_1.14.2
>
> loaded via a namespace (and not attached):
>   [1] affy_1.42.2              affyio_1.32.0            annotate_1.42.0          base64_1.1               BatchJobs_1.2            BBmisc_1.6
>   [7] beanplot_1.1             BiocParallel_0.6.1       biomaRt_2.20.0           biovizBase_1.12.1        bitops_1.0-6             brew_1.0-6
> [13] cluster_1.15.2           codetools_0.2-8          colorspace_1.2-4         dichromat_2.0-0          digest_0.6.4             doRNG_1.6
> [19] fail_1.2                 Formula_1.1-1            genefilter_1.46.1        GenomicAlignments_1.0.1  genoset_1.16.2           gtable_0.1.2
> [25] gtools_3.4.1             Gviz_1.8.3               Hmisc_3.14-4             illuminaio_0.6.0         KernSmooth_2.23-12       latticeExtra_0.6-26
> [31] lumi_2.16.0              Matrix_1.1-4             mclust_4.3               mgcv_1.7-29              multtest_2.20.0          munsell_0.4.2
> [37] nleqslv_2.2              nlme_3.1-117             nor1mix_1.1-4            pkgmaker_0.22            plyr_1.8.1               preprocessCore_1.26.1
> [43] proto_0.3-10             R.methodsS3_1.6.1        RColorBrewer_1.0-5       Rcpp_0.11.2              RCurl_1.95-4.1           registry_0.2
> [49] reshape_0.8.5            rngtools_1.2.4           Rsamtools_1.16.1         rtracklayer_1.24.2       sendmailR_1.1-2          siggenes_1.38.0
> [55] splines_3.1.0            stats4_3.1.0             stringr_0.6.2            survival_2.37-7          tools_3.1.0              VariantAnnotation_1.10.2
> [61] XML_3.98-1.1             xtable_1.7-3             zlibbioc_1.10.0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099