question about package AgiMicroRna
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Hello 1)I need that to implement another normalization between arrays methods like GPA and vsn,LVS,CyclicLoess on the ddTGS(gTotalGeneSignal). 2)I am interest that to obtain an estimate of the gene signal using the RMA algorithm without the function rmaMicroRna ; First I read data into RGlist,then I get BG corrected and normalized between arrays in limma, but I don't know how can to obtain the median of the replicated probes. Please help me. Thanks -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] LVSmiRNA_1.6.0 vsn_3.24.0 MASS_7.3-23 [4] quantreg_5.02 SparseM_1.03 AgiMicroRna_2.6.0 [7] affycoretools_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.18.4 [13] preprocessCore_1.18.0 affy_1.34.0 limma_3.12.3 [16] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 [4] BiocInstaller_1.4.9 biomaRt_2.12.0 Biostrings_2.24.1 [7] Category_2.22.0 gcrma_2.28.0 genefilter_1.38.0 [10] GOstats_2.22.0 graph_1.34.0 grid_2.15.1 [13] GSEABase_1.18.0 IRanges_1.14.4 lattice_0.20-21 [16] RBGL_1.32.1 RCurl_1.95-4.1 stats4_2.15.1 [19] survival_2.37-4 tools_2.15.1 XML_3.98-1.1 [22] xtable_1.7-1 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
Normalization GO vsn Normalization GO vsn • 629 views
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