I am starting to use the DEP
package for analysis of differentially enriched proteins, and so far I am quite happy with it. The vignette is quite good and all the functions worked without issues.
I am however confused about the meaning of the columns in the output results generated by get_df_wide
and get_df_long
:
# Generate a wide data.frame
df_wide <- get_df_wide(dep)
colnames(df_wide)
[1] "name" "Ubi4_1"
[3] "Ubi4_2" "Ubi4_3"
[5] "Ubi6_1" "Ubi6_2"
[7] "Ubi6_3" "Ctrl_1"
[9] "Ctrl_2" "Ctrl_3"
[11] "Ubi1_1" "Ubi1_2"
[13] "Ubi1_3" "Protein.IDs"
[15] "Majority.protein.IDs" "Protein.names"
[17] "Gene.names" "Fasta.headers"
[19] "Peptides" "Razor...unique.peptides"
[21] "Unique.peptides" "Only.identified.by.site"
[23] "Reverse" "Potential.contaminant"
[25] "ID" "imputed"
[27] "num_NAs" "Ubi1_vs_Ctrl_CI.L"
[29] "Ubi1_vs_Ctrl_CI.R" "Ubi1_vs_Ctrl_diff"
[31] "Ubi1_vs_Ctrl_p.adj" "Ubi1_vs_Ctrl_p.val"
[33] "Ubi4_vs_Ctrl_CI.L" "Ubi4_vs_Ctrl_CI.R"
[35] "Ubi4_vs_Ctrl_diff" "Ubi4_vs_Ctrl_p.adj"
[37] "Ubi4_vs_Ctrl_p.val" "Ubi6_vs_Ctrl_CI.L"
[39] "Ubi6_vs_Ctrl_CI.R" "Ubi6_vs_Ctrl_diff"
[41] "Ubi6_vs_Ctrl_p.adj" "Ubi6_vs_Ctrl_p.val"
[43] "Ubi1_vs_Ctrl_significant" "Ubi4_vs_Ctrl_significant"
[45] "Ubi6_vs_Ctrl_significant" "significant"
# Generate a long data.frame
df_long <- get_df_long(dep)
colnames(df_long)
[1] "label" "condition"
[3] "replicate" "name"
[5] "intensity" "Protein.IDs"
[7] "Majority.protein.IDs" "Protein.names"
[9] "Gene.names" "Fasta.headers"
[11] "Peptides" "Razor...unique.peptides"
[13] "Unique.peptides" "Only.identified.by.site"
[15] "Reverse" "Potential.contaminant"
[17] "ID" "imputed"
[19] "num_NAs" "Ubi1_vs_Ctrl_CI.L"
[21] "Ubi1_vs_Ctrl_CI.R" "Ubi1_vs_Ctrl_diff"
[23] "Ubi1_vs_Ctrl_p.adj" "Ubi1_vs_Ctrl_p.val"
[25] "Ubi4_vs_Ctrl_CI.L" "Ubi4_vs_Ctrl_CI.R"
[27] "Ubi4_vs_Ctrl_diff" "Ubi4_vs_Ctrl_p.adj"
[29] "Ubi4_vs_Ctrl_p.val" "Ubi6_vs_Ctrl_CI.L"
[31] "Ubi6_vs_Ctrl_CI.R" "Ubi6_vs_Ctrl_diff"
[33] "Ubi6_vs_Ctrl_p.adj" "Ubi6_vs_Ctrl_p.val"
[35] "Ubi1_vs_Ctrl_significant" "Ubi4_vs_Ctrl_significant"
[37] "Ubi6_vs_Ctrl_significant" "significant"
Specifically what is the difference between, for example, "Ubi4_vs_Ctrl_CI.L"
and `"Ubi4vsCtrl_CI.R". It might be something obvious but I am new to proteomics analysis, so could anyone elucidate me?
Session info:
sessionInfo() | |
R version 3.6.0 (2019-04-26) | |
Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
Running under: macOS Mojave 10.14.5 | |
Matrix products: default | |
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib | |
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib | |
locale: | |
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | |
attached base packages: | |
[1] parallel stats4 stats graphics grDevices utils datasets | |
[8] methods base | |
other attached packages: | |
[1] SummarizedExperiment_1.14.0 DelayedArray_0.10.0 | |
[3] BiocParallel_1.18.0 matrixStats_0.54.0 | |
[5] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 | |
[7] IRanges_2.18.1 S4Vectors_0.22.0 | |
[9] imputeLCMD_2.0 impute_1.58.0 | |
[11] pcaMethods_1.76.0 Biobase_2.44.0 | |
[13] BiocGenerics_0.30.0 norm_1.0-9.5 | |
[15] tmvtnorm_1.4-10 gmm_1.6-2 | |
[17] sandwich_2.5-1 Matrix_1.2-17 | |
[19] mvtnorm_1.0-11 dplyr_0.8.3 | |
[21] DEP_1.6.0 | |
loaded via a namespace (and not attached): | |
[1] colorspace_1.4-1 rjson_0.2.20 rprojroot_1.3-2 | |
[4] circlize_0.4.6 XVector_0.24.0 fs_1.3.1 | |
[7] GlobalOptions_0.1.0 clue_0.3-57 mzR_2.18.0 | |
[10] remotes_2.1.0 affyio_1.54.0 ggrepel_0.8.1 | |
[13] DT_0.7 codetools_0.2-16 ncdf4_1.16.1 | |
[16] doParallel_1.0.14 knitr_1.23 pkgload_1.0.2 | |
[19] zeallot_0.1.0 cluster_2.1.0 vsn_3.52.0 | |
[22] png_0.1-7 shinydashboard_0.7.1 shiny_1.3.2 | |
[25] BiocManager_1.30.4 readr_1.3.1 compiler_3.6.0 | |
[28] backports_1.1.4 assertthat_0.2.1 lazyeval_0.2.2 | |
[31] limma_3.40.2 cli_1.1.0 later_0.8.0 | |
[34] htmltools_0.3.6 prettyunits_1.0.2 tools_3.6.0 | |
[37] gtable_0.3.0 glue_1.3.1 GenomeInfoDbData_1.2.1 | |
[40] affy_1.62.0 Rcpp_1.0.1 MALDIquant_1.19.3 | |
[43] vctrs_0.2.0 preprocessCore_1.46.0 iterators_1.0.10 | |
[46] xfun_0.8 ps_1.3.0 testthat_2.1.1 | |
[49] mime_0.7 devtools_2.1.0 XML_3.98-1.20 | |
[52] zlibbioc_1.30.0 MASS_7.3-51.4 zoo_1.8-6 | |
[55] scales_1.0.0 MSnbase_2.10.1 hms_0.5.0 | |
[58] promises_1.0.1 ProtGenerics_1.16.0 RColorBrewer_1.1-2 | |
[61] ComplexHeatmap_2.0.0 memoise_1.1.0 ggplot2_3.2.0 | |
[64] highr_0.8 desc_1.2.0 foreach_1.4.4 | |
[67] pkgbuild_1.0.3 shape_1.4.4 rlang_0.4.0 | |
[70] pkgconfig_2.0.2 bitops_1.0-6 mzID_1.22.0 | |
[73] lattice_0.20-38 purrr_0.3.2 htmlwidgets_1.3 | |
[76] labeling_0.3 tidyselect_0.2.5 processx_3.4.1 | |
[79] plyr_1.8.4 magrittr_1.5 R6_2.4.0 | |
[82] pillar_1.4.2 withr_2.1.2 RCurl_1.95-4.12 | |
[85] tibble_2.1.3 crayon_1.3.4 fdrtool_1.2.15 | |
[88] usethis_1.5.1 GetoptLong_0.1.7 grid_3.6.0 | |
[91] callr_3.3.1 digest_0.6.20 xtable_1.8-4 | |
[94] tidyr_0.8.3 httpuv_1.5.1 munsell_0.5.0 | |
[97] sessioninfo_1.1.1 |
deleted - wrong spot