[BioC] LumiT VST error

Paolo Kunderfranco paolo.kunderfranco at gmail.com
Tue Mar 13 15:39:43 CET 2012

Hello, i am having problems with VST with my Illumina data,
My values are all positive using lumiB "forcePositive" and my QC plots
looks fine,
Can anyone help me?

> library("lumi")
> fileName<-"ANG.txt"
> x.lumi<-lumiR.batch(fileName)
Inputting the data ...
Annotation columns are not available in the data.
Duplicated IDs found and were merged!

Adding nuID to the data ...
Please provide Illumina ID Mapping library!
Perform Quality Control assessment of the LumiBatch object ...
Warning message:
In as.vector(data) : si è prodotto un NA per coercizione
> lumi.T<-lumiT(x.lumi)
Perform vst transformation ...
2012-03-13 15:33:15 , processing array  1
Errore in if (any(std < 0)) { :
  valore mancante dove è richiesto TRUE/FALSE
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
[5] LC_TIME=Italian_Italy.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_3.6.9    lumi_2.2.1     Biobase_2.10.0

loaded via a namespace (and not attached):
 [1] affy_1.28.1           affyio_1.18.0         annotate_1.28.1
AnnotationDbi_1.12.1  DBI_0.2-5             grid_2.12.1
 [7] hdrcde_2.15           KernSmooth_2.23-4     lattice_0.19-13
MASS_7.3-9            Matrix_0.999375-46    methylumi_1.6.1
[13] mgcv_1.7-2            nlme_3.1-97           preprocessCore_1.12.0
RSQLite_0.10.0        tools_2.12.1          xtable_1.6-0

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