[BioC] lumi package - error while performing VST
Cei Abreu-Goodger
cei at sanger.ac.uk
Thu Feb 7 10:32:18 CET 2008
Hi Yogi,
First, update your Bioc packages... I believe the current version of
lumi is 1.4.0...
Also, try looking at the objects you create before going to the next
step. Is the 'raw' object looking like what you expect?
simply type 'raw', or 'boxplot(raw)'.
Cheers,
Cei
Yogi Sundaravadanam wrote:
> Hi all
>
>
>
> I tried doing VST and the following error occurred and I’m stuck. I’d
> really appreciate any thoughts or suggestions on this please.
>
>
>
>
>> library(lumi)
>>
>
>
>> raw <- lumiR("Sample_Gene_Profile.txt")
>>
>
> Warning messages:
>
> 1: closing unused connection 4 (Sample_Gene_Profile.txt)
>
> 2: closing unused connection 3 (Sample_Gene_Profile.txt)
>
>
>> lumi.T <- lumiT(raw)
>>
>
> 2008-02-07 09:29:07 , processing array 1
>
> Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
>
>
> 0 (non-NA) cases
>
>
>
>
>
>
>> sessionInfo()
>>
>
> R version 2.6.0 (2007-10-03)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
> ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
>
>
> attached base packages:
>
> [1] tools stats graphics grDevices utils datasets methods
>
>
> [8] base
>
>
>
> other attached packages:
>
> [1] limma_2.12.0 lumi_1.2.0 annotate_1.16.1
>
> [4] xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4
>
> [7] DBI_0.2-4 mgcv_1.3-27 affy_1.16.0
>
> [10] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1
>
>
>
> Thanks heaps
>
> Yogi
>
>
>
>
>
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--
Cei Abreu-Goodger, PhD
Wellcome Trust Sanger Institute
Computational and Functional Genomics
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SA, UK
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
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