> cgh_test
Instance of class rCGH-Agilent
Dataset with 132452 probes and 7 columns.
Array information:
info
fileName US45102933_254852310046_S01_CytoCGH_0209_4x_Mar14_1_1.txt
sampleName <NA>
labName <NA>
platform Agilent
suppressFlags TRUE
genome hg19
barCode 254852310046_1_1
gridName 048523_20130328
scanDate 2015-11-04
programVersion CytoCGH_0209_4x_Mar14 (Read Only)
gridGenomicBuild hg19:GRCh37:Feb2009
reference Dual color hybridization
analyseDate 2016-06-06
rCGH_version 1.2.2
> cgh_test = adjustSignal(cgh_test, Ref="cy5")
Recall you are using cy5 as reference.
Cy effect adjustment...
GC% adjustment...
Error in .dlrs(cnSet$Log2Ratio) : Vector length>2 needed for computation
> traceback()
4: stop("Vector length>2 needed for computation")
3: .dlrs(cnSet$Log2Ratio)
2: adjustSignal(cgh_test, Ref = "cy5")
1: adjustSignal(cgh_test, Ref = "cy5")
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed (20160603) (x86_64)
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rCGH_1.2.2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5
[2] BiocInstaller_1.22.2
[3] plyr_1.8.3
[4] GenomeInfoDb_1.8.1
[5] XVector_0.12.0
[6] GenomicFeatures_1.24.2
[7] bitops_1.0-6
[8] tools_3.3.0
[9] zlibbioc_1.18.0
[10] mclust_5.2
[11] biomaRt_2.28.0
[12] digest_0.6.9
[13] preprocessCore_1.34.0
[14] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[15] RSQLite_1.0.0
[16] gtable_0.2.0
[17] lattice_0.20-33
[18] Matrix_1.2-6
[19] shiny_0.13.2
[20] DBI_0.4-1
[21] parallel_3.3.0
[22] cluster_2.0.4
[23] rtracklayer_1.32.0
[24] Biostrings_2.40.1
[25] S4Vectors_0.10.1
[26] IRanges_2.6.0
[27] multtest_2.28.0
[28] stats4_3.3.0
[29] grid_3.3.0
[30] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[31] Biobase_2.32.0
[32] R6_2.1.2
[33] AnnotationDbi_1.34.3
[34] DNAcopy_1.46.0
[35] survival_2.39-4
[36] BiocParallel_1.6.2
[37] XML_3.98-1.4
[38] limma_3.28.5
[39] ggplot2_2.1.0
[40] org.Hs.eg.db_3.3.0
[41] MASS_7.3-45
[42] splines_3.3.0
[43] GenomicAlignments_1.8.1
[44] scales_0.4.0
[45] Rsamtools_1.24.0
[46] htmltools_0.3.5
[47] BiocGenerics_0.18.0
[48] GenomicRanges_1.24.1
[49] SummarizedExperiment_1.2.2
[50] TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.3
[51] mime_0.4
[52] xtable_1.8-2
[53] colorspace_1.2-6
[54] httpuv_1.3.3
[55] aCGH_1.50.0
[56] affy_1.50.0
[57] RCurl_1.95-4.8
[58] munsell_0.4.3
[59] affyio_1.42.0
