[BioC] lumi package - error while performing VST

[Cei Abreu-Goodger]

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 
>
>  
>
>  
>
>   _____  
>
>  Please Note: The message is intended only for the addressee. If you
> receive this message in error please do not publish, distribute, or copy
> it. Please advise the AGRF by telephone or email, and delete this
> message from your computer. 
>
>  
>
>
>
> 	[[alternative HTML version deleted]]
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
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 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.