"R.version.3.4.0..2017.04.21." "Platform: x86_64-apple-darwin15.6.0 (64-bit)" "Running under: OS X El Capitan 10.11.6" "Matrix products: default" "BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib" "LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] MSstats_3.8.2 BiocInstaller_1.26.0" "loaded via a namespace (and not attached):" " [1] Rcpp_0.12.11 nloptr_1.0.4 compiler_3.4.0 plyr_1.8.4 bitops_1.0-6 " " [6] ProtGenerics_1.8.0 iterators_1.0.8 tools_3.4.0 zlibbioc_1.22.0 MALDIquant_1.16.2 " "[11] digest_0.6.12 lme4_1.1-13 preprocessCore_1.38.1 tibble_1.3.3 gtable_0.2.0 " "[16] nlme_3.1-131 lattice_0.20-35 rlang_0.1.1 Matrix_1.2-10 foreach_1.4.3 " "[21] ggrepel_0.6.5 parallel_3.4.0 stringr_1.2.0 caTools_1.17.1 gtools_3.5.0 " "[26] S4Vectors_0.14.3 IRanges_2.10.2 stats4_3.4.0 grid_3.4.0 Biobase_2.36.2 " "[31] impute_1.50.1 marray_1.54.0 survival_2.41-3 XML_3.98-1.9 BiocParallel_1.10.1 " "[36] minpack.lm_1.2-1 gdata_2.18.0 minqa_1.2.4 limma_3.32.2 magrittr_1.5 " "[41] reshape2_1.4.2 ggplot2_2.2.1 mzR_2.10.0 gplots_3.0.1 scales_0.4.1 " "[46] pcaMethods_1.68.0 codetools_0.2-15 BiocGenerics_0.22.0 splines_3.4.0 MASS_7.3-47 " "[51] mzID_1.14.0 MSnbase_2.2.0 colorspace_1.3-2 KernSmooth_2.23-15 stringi_1.1.5 " "[56] affy_1.54.0 lazyeval_0.2.0 munsell_0.4.3 doParallel_1.0.10 vsn_3.44.0 " "[61] affyio_1.46.0 " " " " " "MSstats - dataProcess function" " " "The required input : provided - okay" "summaryMethod : TMP" "cutoffCensored : minFeature" "censoredInt : NA" "New input format : made new columns for analysis - okay" "** There are1295 intensities which are zero. These intensities are replaced with 1." "Logarithm transformation: log2 transformation is done - okay" "Multiple fractionations are existed : 1 fractionations per MS replicate."