[BioC] create the expression set
Jia, Li (NIH/NCI) [C]
li.jia2 at nih.gov
Thu Jun 26 22:08:29 CEST 2014
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.
Thanks,
Li
On 6/26/14 2:51 PM, "James W. MacDonald" <jmacdon at 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
>>‘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
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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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
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