search

berndbischl / BBmisc

Other
20 stars 7 forks source link

normalize function giving error #86

Closed boseb closed 5 years ago

boseb commented 5 years ago

Hi, I am normalizing a dataframe but normalize function is giving error

x<- matrix(1:9,3,3) x [,1] [,2] [,3] [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 normalize(x, method = "standardize", range = c(0, 1), margin = 2L, on.constant = "quiet") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘normalize’ for signature ‘"matrix"’

please help

berndbischl commented 5 years ago

There is a very clear error message which you simply need to read? Hint. You are not passing a Df.

boseb commented 5 years ago

Hi, I am very sure I am giving dataframe for my actual work, I just tried to gave you a simple example. Anyways, check it again please,

x<-data.frame(x)

x X1 X2 X3 1 1 4 7 2 2 5 8 3 3 6 9 normalize(x, method = "range", range = c(0, 1), margin = 2L, on.constant = "quiet") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘normalize’ for signature ‘"data.frame"’

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages: [1] zoo_1.8-6 foreign_0.8-71 sp_1.3-1 limma_3.40.6
[5] SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1 matrixStats_0.55.0
[9] Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.2
[13] S4Vectors_0.22.1 BiocGenerics_0.30.0 TCGAbiolinks_2.13.6 tidyr_1.0.0
[17] caret_6.0-84 ggplot2_3.2.1 lattice_0.20-38 biomaRt_2.41.8
[21] xlsx_0.6.1 CePa_0.6 pbapply_1.4-1 reshape2_1.4.3
[25] reshape_0.8.8 sqldf_0.4-11 RSQLite_2.1.2 gsubfn_0.7
[29] proto_1.0.0 data.table_1.12.2 plyr_1.8.4 stringr_1.4.0
[33] janitor_1.1.1 glmnet_2.0-18 foreach_1.4.7 Matrix_1.2-17
[37] readr_1.3.1 BBmisc_1.11 svdvis_0.1

loaded via a namespace (and not attached): [1] R.utils_2.9.0 tidyselect_0.2.5 AnnotationDbi_1.46.1 grid_3.6.0
[5] devtools_2.0.1 DESeq_1.36.0 munsell_0.5.0 codetools_0.2-16
[9] chron_2.3-54 withr_2.1.2 colorspace_1.4-1 knitr_1.24
[13] rstudioapi_0.10 ggsignif_0.6.0 rJava_0.9-11 GenomeInfoDbData_1.2.1
[17] hwriter_1.3.2 KMsurv_0.1-5 bit64_0.9-7 rprojroot_1.3-2
[21] downloader_0.4 vctrs_0.2.0 generics_0.0.2 ipred_0.9-8
[25] xfun_0.9 ggthemes_4.2.0 BiocFileCache_1.6.0 EDASeq_2.18.0
[29] R6_2.4.0 doParallel_1.0.15 clue_0.3-57 locfit_1.5-9.1
[33] bitops_1.0-6 assertthat_0.2.1 scales_1.0.0 nnet_7.3-12
[37] gtable_0.3.0 sva_3.32.1 processx_3.3.0 timeDate_3043.102
[41] rlang_0.4.0 zeallot_0.1.0 genefilter_1.66.0 GlobalOptions_0.1.0
[45] splines_3.6.0 rtracklayer_1.44.4 lazyeval_0.2.2 ModelMetrics_1.2.2
[49] selectr_0.4-1 broom_0.5.2 checkmate_1.9.4 yaml_2.2.0
[53] GenomicFeatures_1.36.4 backports_1.1.4 usethis_1.4.0 tools_3.6.0
[57] lava_1.6.6 tcltk_3.6.0 RColorBrewer_1.1-2 sessioninfo_1.1.1
[61] Rcpp_1.0.2 progress_1.2.2 zlibbioc_1.30.0 purrr_0.3.2
[65] RCurl_1.95-4.12 ps_1.3.0 prettyunits_1.0.2 ggpubr_0.2.3
[69] rpart_4.1-15 openssl_1.4.1 GetoptLong_0.1.7 ggrepel_0.8.1
[73] cluster_2.0.8 fs_1.2.7 magrittr_1.5 circlize_0.4.8
[77] survminer_0.4.6 pkgload_1.0.2 aroma.light_3.14.0 hms_0.5.1
[81] xlsxjars_0.6.1 xtable_1.8-4 XML_3.98-1.20 gridExtra_2.3
[85] shape_1.4.4 testthat_2.0.1 compiler_3.6.0 tibble_2.1.3
[89] crayon_1.3.4 R.oo_1.22.0 mgcv_1.8-28 geneplotter_1.62.0
[93] lubridate_1.7.4 DBI_1.0.0 dbplyr_1.3.0 matlab_1.0.2
[97] ComplexHeatmap_2.0.0 MASS_7.3-51.4 rappdirs_0.3.1 ShortRead_1.42.0
[101] cli_1.1.0 R.methodsS3_1.7.1 gower_0.2.1 igraph_1.2.4.1
[105] pkgconfig_2.0.2 km.ci_0.5-2 GenomicAlignments_1.20.1 recipes_0.1.6
[109] xml2_1.2.2 annotate_1.62.0 XVector_0.24.0 prodlim_2018.04.18
[113] rvest_0.3.4 callr_3.2.0 digest_0.6.20 ConsensusClusterPlus_1.48.0 [117] graph_1.62.0 Biostrings_2.52.0 survMisc_0.5.5 edgeR_3.26.8
[121] curl_4.0 Rsamtools_2.0.0 rjson_0.2.20 lifecycle_0.1.0
[125] nlme_3.1-139 jsonlite_1.6 desc_1.2.0 askpass_1.1
[129] pillar_1.4.2 GGally_1.4.0 httr_1.4.1 pkgbuild_1.0.3
[133] survival_2.44-1.1 remotes_2.1.0 glue_1.3.1 png_0.1-7
[137] iterators_1.0.12 bit_1.1-14 Rgraphviz_2.26.0 class_7.3-15
[141] stringi_1.4.3 blob_1.2.0 latticeExtra_0.6-28 memoise_1.1.0
[145] dplyr_0.8.3