[BioC] Problem with BGandNorm() from the Agi4x44PreProcess package
Marco Fabbri
fabbri.marco at gmail.com
Thu Apr 12 17:46:33 CEST 2012
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
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