On Thu, Jun 26, 2014 at 4:08 PM, Jia, Li (NIH/NCI) [C] <li.jia2@nih.gov>
wrote:

> Thanks Jim for the reply!
>
> I don't proceed to lmFit on limma, I only need to generate ExpressionSet
> and use it for the SOM.
>

Hi, Li.

You probably do not need an ExpressionSet for SOM, either.  However, you
can generate a minimal one by doing:

Dset = ExpressionSet(assayData=normdata)

You can probably add phenoData using:

pData(Dset) = pheno

Sean



>
> Thanks,
> Li
>
> On 6/26/14 2:51 PM, "James W. MacDonald" <jmacdon@uw.edu> wrote:
>
> >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
> >>â€˜annotatedDataFrameFromâ€™ for signature â€˜"data.frame"â€™
> >>
> >> 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
> >>
> >> --
> >> Sent via the guest posting facility at bioconductor.org.
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >>http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >--
> >James W. MacDonald, M.S.
> >Biostatistician
> >University of Washington
> >Environmental and Occupational Health Sciences
> >4225 Roosevelt Way NE, # 100
> >Seattle WA 98105-6099
>
> _______________________________________________
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