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:

sessionInfo()
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

locale:
[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                                        org.Hs.eg.db_3.5.0                                 
[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

Laura