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Question: NOISeq error message while using ARSyNseq batch correction function
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gravatar for lina.faller
2.1 years ago by
lina.faller0 wrote:

Hi all,

I am trying to run the ARSyNseq function to correct a batch effect but am running into an error (see below).

If anyone has an idea where this is coming from, let me know!

Best,

~Lina

> mydatacorr1 = ARSyNseq(mydata, factor = "date", batch = TRUE, norm = "tmm", logtransf = FALSE)
Error in if (all(obs == ref)) return(1) :
  missing value where TRUE/FALSE needed

> mydata
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35693 features, 11 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: AT_6 AT_7 ... AT_387 (11 total)
  varLabels: condition date
  varMetadata: labelDescription
featureData
  featureNames: VBIPreBuc139135_1403 VBIActSp171359_1532 ...
    VBILepSp252191_1789 (35693 total)
  fvarLabels: Length
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] NOISeq_2.14.0       Matrix_1.2-2        Biobase_2.28.0     
[4] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] tools_3.2.2     grid_3.2.2      lattice_0.20-33

 

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