[BioC] Bioconductor Digest, Vol 109, Issue 14

[Pan Du]

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
>
>