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msstats-8.log
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msstats-8.log
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"R.version.3.5.0..2018.04.23."
"Platform: x86_64-apple-darwin15.6.0 (64-bit)"
"Running under: macOS 10.14.1"
"Matrix products: default"
"BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib"
"LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] stats graphics grDevices utils datasets methods base "
"other attached packages:"
"[1] bindrcpp_0.2.2 MSstats_3.12.3"
"loaded via a namespace (and not attached):"
" [1] gtools_3.8.1 minpack.lm_1.2-1 tidyselect_0.2.5 reshape2_1.4.3 "
" [5] purrr_0.2.5 splines_3.5.0 lattice_0.20-38 colorspace_1.3-2 "
" [9] doSNOW_1.0.16 snow_0.4-3 yaml_2.2.0 survival_2.43-3 "
"[13] marray_1.58.0 rlang_0.3.0.1 nloptr_1.2.1 pillar_1.3.0 "
"[17] glue_1.3.0 foreach_1.4.4 bindr_0.1.1 plyr_1.8.4 "
"[21] stringr_1.3.1 munsell_0.5.0 gtable_0.2.0 caTools_1.17.1.1 "
"[25] codetools_0.2-15 parallel_3.5.0 preprocessCore_1.42.0 Rcpp_1.0.0 "
"[29] KernSmooth_2.23-15 scales_1.0.0 limma_3.36.5 gdata_2.18.0 "
"[33] lme4_1.1-19 gplots_3.0.1 ggplot2_3.1.0 stringi_1.2.4 "
"[37] dplyr_0.7.8 ggrepel_0.8.0 grid_3.5.0 tools_3.5.0 "
"[41] bitops_1.0-6 magrittr_1.5 lazyeval_0.2.1 tibble_1.4.2 "
"[45] randomForest_4.6-14 tidyr_0.8.2 crayon_1.3.4 pkgconfig_2.0.2 "
"[49] MASS_7.3-51.1 Matrix_1.2-15 data.table_1.11.8 assertthat_0.2.0 "
"[53] minqa_1.2.4 rstudioapi_0.8 iterators_1.0.10 R6_2.3.0 "
"[57] nlme_3.1-137 compiler_3.5.0 "
" "
" "
"MSstats - dataProcess function"
" "
"The required input : provided - okay"
"summaryMethod : TMP"
"cutoffCensored : minFeature"
"censoredInt : 0"
"New input format : made new columns for analysis - okay"
"** There are 4379 intensities which are zero. These intensities are replaced with 1."
"Logarithm transformation: log2 transformation is done - okay"