Question

Error in champ.CNA (v. 2.6.0)

0

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rasmus.rydbirk ▴ 10

@rasmusrydbirk-12534

Last seen 4.9 years ago

While testing the ChAMP library i came upon this error, when running champ.CNA:

<< Processing Groups >>
Error in intsqnlogratio[, which(pheno == groups[g])] :
subscript out of bounds

If I set

groupFreqPlots=FALSE

I don't get the error.

I've tried setting the control group to both "C" and "CTRL" and of course updating

controlGroup=""

correspondingly.

Also, i can't open the .JPEG files that are created as the output.

Any help is greatly appreciated. Thank you!

champ • 1.6k views

ADD COMMENT • link updated 6.1 years ago by elmori • 0 • written 7.1 years ago by rasmus.rydbirk ▴ 10

0

Entering edit mode

Additional information:

BiocInstaller::biocValid() is OK.

traceback():

1: champ.CNA(intensity = myLoad$intensity, controlGroup = "CTRL",
sampleCNA = FALSE, groupFreqPlots = TRUE, Rplot = FALSE,
arraytype = "EPIC")

sessionInfo():

R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

attached base packages:

[1] splines stats4 parallel stats graphics grDevices utils datasets methods
[10] base

other attached packages:
[1] ChAMP_2.6.0 IlluminaHumanMethylationEPICmanifest_0.3.0
[3] Illumina450ProbeVariants.db_1.10.0 DMRcate_1.10.7
[5] DMRcatedata_1.10.1 DSS_2.14.0
[7] bsseq_1.10.0 FEM_3.2.0
[9] graph_1.52.0 org.Hs.eg.db_3.4.0
[11] impute_1.48.0 igraph_1.0.1
[13] corrplot_0.77 marray_1.52.0
[15] limma_3.30.12 Matrix_1.2-8
[17] AnnotationDbi_1.36.2 ChAMPdata_2.6.0
[19] minfi_1.20.2 bumphunter_1.14.0
[21] locfit_1.5-9.1 iterators_1.0.8
[23] foreach_1.4.3 Biostrings_2.42.1
[25] XVector_0.14.0 SummarizedExperiment_1.4.0
[27] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3
[29] IRanges_2.8.1 S4Vectors_0.12.1
[31] Biobase_2.34.0 BiocGenerics_0.20.0

loaded via a namespace (and not attached):
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ADD REPLY • link 7.1 years ago rasmus.rydbirk ▴ 10

score 0 · Answer 1 · 2018-03-27

For those of you coming upon this, this occurs when doing groupFreqPlots, and not when doing sampleCNA, as rasmus notes. It occurs when control is specified, because intsqnlogratio only contains columns for the non-control groups, but groups still has the control labels. A temporary fix would be:

data_group=intsqnlogratio[,which(pheno == groups[g])]

becoming

ncpheno = pheno[!pheno %in% controlGroup] data_group=intsqnlogratio[,which(ncpheno == groups[g])]

and continue using ncpheno in rows 111 and 114.