Question: Problem with BGandNorm() from the Agi4x44PreProcess package
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gravatar for marco fabbri
7.1 years ago by
marco fabbri320
Italy
marco fabbri320 wrote:
I have a problem BGandNorm() from Agi4x44PreProcess package > ddNORM=BGandNorm(ag1,BGmethod="half",NORMmethod="vsn", + foreground="MeanSignal",background="BGMedianSignal", + offset=50,makePLOTpre=FALSE,makePLOTpost=FALSE) BACKGROUND CORRECTION AND NORMALIZATION foreground: MeanSignal background: BGMedianSignal Error in normalizeBetweenArrays(ddBG$G, method = NORMmethod) : vsn method no longer supported. Please use normalizeVSN instead. > ddNORM=BGandNorm(ag1,BGmethod="half",NORMmethod="normalizeVSN", + foreground="MeanSignal",background="BGMedianSignal", + offset=50,makePLOTpre=FALSE,makePLOTpost=FALSE) BACKGROUND CORRECTION AND NORMALIZATION Error in BGandNorm(ag1, BGmethod = "half", NORMmethod = "normalizeVSN", : NORMmethod should be one of 'none', 'quantile','vsn' > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.22.0 Agi4x44PreProcess_1.14.0 genefilter_1.36.0 [4] annotate_1.32.3 limma_3.10.3 hgug4112a.db_2.6.3 [7] org.Hs.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 [10] AnnotationDbi_1.16.19 Biobase_2.14.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] affy_1.32.1 affyio_1.22.0 grid_2.14.2 [4] IRanges_1.12.6 lattice_0.20-0 preprocessCore_1.16.0 [7] splines_2.14.2 survival_2.36-12 tools_2.14.2 [10] xtable_1.7-0 zlibbioc_1.0.1 Thank you\\Marco
vsn agi4x44preprocess • 418 views
ADD COMMENTlink written 7.1 years ago by marco fabbri320
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