[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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