[BioC] LumiT VST error
Pan Du
dupan.mail at gmail.com
Wed Mar 14 16:11:19 CET 2012
Hi Paolo
Please update your R and lumi package. I remember this was fixed a while ago.
Pan
> Date: Tue, 13 Mar 2012 15:39:43 +0100
> From: Paolo Kunderfranco <paolo.kunderfranco at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] LumiT VST error
> Message-ID:
> <CAGxWFc9iXXHJcDvDCTAkUCHJZGCoSxg_t7nCOOZBF=Ef_cubMQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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?
> Thanks,
> Paolo
>
>
>> 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 ? 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 ? richiesto TRUE/FALSE
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
> LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
> [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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