Question: ChAMP functional normalization error "subscript out of bounds"
gravatar for Laura
17 months ago by
Laura0 wrote:

Hello everyone,

Using ChAMP to Analyse my EPIC Array data I am struggeling with functional normalization.

I load my data using the minfi method to ensure that rgset and mset are present.

myLoad<- champ.load(directory = test.dir, arraytype = "EPIC", method = "minfi", force = TRUE)

For some datasets functional normalization works well but in two datasets I got the following error:

myNorm<- champ.norm(arraytype = "EPIC", method="FunctionalNormalization")
[>>>>> ChAMP.NORM START <<<<<<]
champ.norm Results will be saved in ./CHAMP_Normalization/
[ SWAN method call for BOTH rgSet and mset input, FunctionalNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
Error in getBeta(preprocessFunnorm(rgSet))[rownames(beta), ] : 
  subscript out of bounds
In addition: Warning message:
In dir.create(resultsDir) : '.\CHAMP_Normalization' already exists

Please find my session info here:

R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.28.0                                IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0
 [3] ChAMP_2.9.10                                        IlluminaHumanMethylationEPICmanifest_0.3.0         
 [5] Illumina450ProbeVariants.db_1.14.0                  DMRcate_1.14.0                                     
 [7] DMRcatedata_1.14.0                                  DSS_2.26.0                                         
 [9] bsseq_1.14.0                                        FEM_3.6.0                                          
[11] graph_1.56.0                                                               
[13] impute_1.52.0                                       igraph_1.2.1                                       
[15] corrplot_0.84                                       marray_1.56.0                                      
[17] limma_3.34.9                                        Matrix_1.2-14                                      
[19] AnnotationDbi_1.40.0                                ChAMPdata_2.10.0                                   
[21] minfi_1.24.0                                        bumphunter_1.20.0                                  
[23] locfit_1.5-9.1                                      iterators_1.0.9                                    
[25] foreach_1.4.4                                       Biostrings_2.46.0                                  
[27] XVector_0.18.0                                      SummarizedExperiment_1.8.1                         
[29] DelayedArray_0.4.1                                  matrixStats_0.53.1                                 
[31] Biobase_2.38.0                                      GenomicRanges_1.30.3                               
[33] GenomeInfoDb_1.14.0                                 IRanges_2.12.0                                     
[35] S4Vectors_0.16.0                                    BiocGenerics_0.24.0                                

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) : DESCRIPTION von Paket 'tidyr' fehlt oder zerstört
2: In FUN(X[[i]], ...) :
  DESCRIPTION von Paket 'nleqslv' fehlt oder zerstört
3: In FUN(X[[i]], ...) :
  DESCRIPTION von Paket 'stringi' fehlt oder zerstört

SWAN, BMIQ and PBC normalization work quite well.

May anyone has a suggestion how to fix that problem? I would highly appreciate that.

Many thanks in advance and best wishes


ADD COMMENTlink written 17 months ago by Laura0

Hi Laura, 

I met the same problem while using FunctionalNormalization, but SWAN, BMIQ and PBC can work fine. Have your problem solved?

Thank you so much.


ADD REPLYlink written 12 months ago by yuabrahamliu0
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