[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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