Entering edit mode
Hello All,
I would like to combine 2 ExpressionSet objects into one dataset.
My objects have identical numbers of featureNames, distinct sampleNames, identical pData variables and identical annotation.
Any help is highly appreciated.
Thank you in advance.
Anita
eset1:
ExpressionSet (storageMode: lockedEnvironment) assayData: 24600 features, 16 samples element names: exprs protocolData rowNames: 0215F-02_01AD1_(MTA-1_0).CEL 0215F-02_WT1_(MTA-1_0).CEL ... 0215F-02_19-AD4_(MTA-1_0).CEL (16 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: 0215F-02_01AD1_(MTA-1_0).CEL 0215F-02_WT1_(MTA-1_0).CEL ... 0215F-02_19-AD4_(MTA-1_0).CEL (16 total) varLabels: Affym_R_pheno_ID Nanosting_ID .. (24 total) varMetadata: labelDescription featureData featureNames: TC0100000005.mm.1 TC0100000014.mm.1 ... TSUnmapped00000186.mm.1 (24600 total) fvarLabels: ID Symbol ... Entrez (5 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: mta10sttranscriptcluster.db
eset2
ExpressionSet (storageMode: lockedEnvironment) assayData: 24600 features, 10 samples element names: exprs protocolData rowNames: 0615F-03_CR5x435_(MTA-1_0).CEL 0615F-03_CR5x437_(MTA-1_0).CEL ... 0615F-03_D_201_(MTA-1_0).CEL (10 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: 0615F-03_CR5x435_(MTA-1_0).CEL 0615F-03_CR5x437_(MTA-1_0).CEL ... 0615F-03_D_201_(MTA-1_0).CEL (10 total) varLabels: Affym_R_pheno_ID Nanosting_ID ..(24 total) varMetadata: labelDescription featureData featureNames: TC0100000005.mm.1 TC0100000014.mm.1 ... TSUnmapped00000186.mm.1 (24600 total) fvarLabels: ID Symbol ... Entrez (5 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: mta10sttranscriptcluster.db
code:
> esets <- consolidate(eset1, eset2) or esets <- list(eset1, eset2)
> library(inSilicoMerging)
> eset_COMBAT = merge(esets, method="COMBAT"); Error in data.frame(<S4 object of class "ExpressionSet">, <S4 object of class "ExpressionSet">, : arguments imply differing number of rows: 16, 10
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.46.1 annotate_1.46.1 XML_3.98-1.3 RColorBrewer_1.1-2 [5] corrplot_0.73 Heatplus_2.14.0 pd.mta.1.0_3.12.0 oligo_1.32.0 [9] Biostrings_2.36.1 XVector_0.8.0 WGCNA_1.47 fastcluster_1.1.16 [13] impute_1.42.0 doParallel_1.0.8 iterators_1.0.7 foreach_1.4.2 [17] reshape_0.8.5 Hmisc_3.16-0 Formula_1.2-1 survival_2.38-3 [21] lattice_0.20-33 flashClust_1.01-2 dynamicTreeCut_1.62 cluster_2.0.1 [25] mta10sttranscriptcluster.db_8.3.1 org.Mm.eg.db_3.1.2 AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1 [29] IRanges_2.2.5 S4Vectors_0.6.1 biomaRt_2.24.0 convert_1.44.0 [33] marray_1.46.0 gplots_2.17.0 ggplot2_1.0.1 GGally_0.5.0 [37] hwriter_1.3.2 ReportingTools_2.8.0 RSQLite_1.0.0 DBI_0.3.1 [41] knitr_1.10.5 oligoClasses_1.30.0 limma_3.24.13 sva_3.14.0 [45] genefilter_1.50.0 mgcv_1.8-6 nlme_3.1-121 inSilicoMerging_1.12.0 [49] Biobase_2.28.0 BiocGenerics_0.14.0 loaded via a namespace (and not attached): [1] colorspace_1.2-6 biovizBase_1.16.0 futile.logger_1.4.1 RcppArmadillo_0.5.200.1.0 GenomicRanges_1.20.5 dichromat_2.0-0 [7] affyio_1.36.0 codetools_0.2-14 splines_3.2.0 R.methodsS3_1.7.0 ggbio_1.16.1 geneplotter_1.46.0 [13] Rsamtools_1.20.4 GO.db_3.1.2 R.oo_1.19.0 graph_1.46.0 GOstats_2.34.0 Matrix_1.2-0 [19] acepack_1.3-3.3 tools_3.2.0 gtable_0.1.2 Category_2.34.2 affxparser_1.40.0 reshape2_1.4.1 [25] Rcpp_0.11.6 preprocessCore_1.30.0 gdata_2.17.0 rtracklayer_1.28.6 stringr_1.0.0 proto_0.3-10 [31] gtools_3.5.0 edgeR_3.10.2 zlibbioc_1.14.0 MASS_7.3-43 scales_0.2.5 BSgenome_1.36.2 [37] VariantAnnotation_1.14.6 BiocInstaller_1.18.3 RBGL_1.44.0 lambda.r_1.1.7 gridExtra_2.0.0 rpart_4.1-10 [43] latticeExtra_0.6-26 stringi_0.5-5 GenomicFeatures_1.20.1 caTools_1.17.1 BiocParallel_1.2.9 matrixStats_0.14.2 [49] bitops_1.0-6 GenomicAlignments_1.4.1 bit_1.1-12 GSEABase_1.30.2 AnnotationForge_1.10.1 plyr_1.8.3 [55] magrittr_1.5 DESeq2_1.8.1 foreign_0.8-63 RCurl_1.95-4.7 nnet_7.3-9 futile.options_1.0.0 [61] KernSmooth_2.23-14 OrganismDbi_1.10.0 PFAM.db_3.1.2 locfit_1.5-9.1 digest_0.6.8 xtable_1.7-4 [67] ff_2.2-13 R.utils_2.1.0 munsell_0.4.2 |
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When providing code, please give us exactly what code you used. For instance this line
Is super unhelpful, because nobody knows what you did. I have never heard of the consolidate() function, so have no idea what it does, nor why you would use it in lieu of list(). In addition, which one did you use? The code you supply should be clarifying, not mystifying.
In addition, it is helpful to give the output from running traceback() right after the error, so people can see where the error occured.