Question about lumiT warning message
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clevy ▴ 10
@clevy-8586
Last seen 4.6 years ago
United States

I am attempting to transform a lumiBatch and got the following warning message:

Warning message:
In lumiT(B.complete.RAW.lumi) :
  Too few probes are detectable based on detection p-values!
 
                        Iteration method will be used for VST.

I realize that this is a warning and not an error so I could proceed but I would like to know the criteria for triggering the warning.  I did not find a description of the "Iteration method" in the lumi documentation ( but may have missed it).

 Prior to transformation, I read in the raw data and background corrected with no errors or warnings. Here is the info about the lumiBatch up until the VST:

Summary of data information:

Major Operation History:
[1] submitted   finished    command     lumiVersion
<0 rows> (or 0-length row.names)

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 47323 features, 26 samples 
  element names: detection, exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: 1B 1C ... 6D (26 total)
  varLabels: TissueID Time Treatment
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
Control Data: N/A
QC information: Please run summary(x, 'QC') for details!

 

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] limma_3.22.7        lumi_2.18.0         Biobase_2.26.0     
[4] BiocGenerics_0.12.1 dplyr_0.4.3        

loaded via a namespace (and not attached):
 [1] affy_1.44.0             affyio_1.34.0          
 [3] annotate_1.44.0         AnnotationDbi_1.28.2   
 [5] assertthat_0.1          base64_1.1             
 [7] base64enc_0.1-3         BatchJobs_1.6          
 [9] BBmisc_1.9              beanplot_1.2           
[11] BiocInstaller_1.16.5    BiocParallel_1.0.3     
[13] biomaRt_2.22.0          Biostrings_2.34.1      
[15] bitops_1.0-6            brew_1.0-6             
[17] bumphunter_1.6.0        checkmate_1.6.2        
[19] codetools_0.2-14        colorspace_1.2-6       
[21] DBI_0.3.1               digest_0.6.8           
[23] doRNG_1.6               fail_1.2               
[25] foreach_1.4.2           genefilter_1.48.1      
[27] GenomeInfoDb_1.2.5      GenomicAlignments_1.2.2
[29] GenomicFeatures_1.18.7  GenomicRanges_1.18.4   
[31] grid_3.1.2              htmltools_0.2.6        
[33] illuminaio_0.8.0        IRanges_2.0.1          
[35] iterators_1.0.7         KernSmooth_2.23-15     
[37] lattice_0.20-29         locfit_1.5-9.1         
[39] magrittr_1.5            MASS_7.3-44            
[41] Matrix_1.2-2            matrixStats_0.14.2     
[43] mclust_5.0.2            methylumi_2.12.0       
[45] mgcv_1.8-7              minfi_1.12.0           
[47] multtest_2.22.0         nleqslv_2.8            
[49] nlme_3.1-122            nor1mix_1.2-1          
[51] pkgmaker_0.22           plyr_1.8.3             
[53] preprocessCore_1.28.0   quadprog_1.5-5         
[55] R6_2.1.1                RColorBrewer_1.1-2     
[57] Rcpp_0.12.0             RCurl_1.95-4.7         
[59] registry_0.3            reshape_0.8.5          
[61] rmarkdown_0.8           rngtools_1.2.4         
[63] Rsamtools_1.18.3        RSQLite_1.0.0          
[65] rtracklayer_1.26.3      S4Vectors_0.4.0        
[67] sendmailR_1.2-1         siggenes_1.40.0        
[69] splines_3.1.2           stats4_3.1.2           
[71] stringi_0.5-5           stringr_1.0.0          
[73] survival_2.38-3         tools_3.1.2            
[75] XML_3.98-1.3            xtable_1.7-4           
[77] XVector_0.6.0           yaml_2.1.13            
[79] zlibbioc_1.12.0   

 

Thanks in advance for any advice!

Claire Levy

University of Washing OBGYN/Fred Hutchinson Cancer Research Center VIDD

Seattle, WA

lumi • 879 views
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