[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



-- 
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