Entering edit mode
Laura
•
0
@laura-15853
Last seen 6.5 years ago
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
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.
Yu