
Attaching package: 'plyr'

The following objects are masked from 'package:reshape':

    rename, round_any


Attaching package: 'data.table'

The following object is masked from 'package:reshape':

    melt


Attaching package: 'pryr'

The following object is masked from 'package:data.table':

    address

    +-- Reading input data ... [ 32.2 MB used ]
       +-- Reading data file ... [ 0.1s elapsed, 32.2 MB used ]
Warning in `[.data.table`(tmp.table.2, , `:=`(c("Protein.IDs", "Protein.Names"),  :
  Adding new column 'Protein.Names' then assigning NULL (deleting it).
       +-- read.pgroups_v3: Identified proteins: 896 (AFCat1) [ +2.4s, 2.6s elapsed, 56.6 MB used ]
       +-- read.pgroups_v3: Discarded PSM records due to unassigned protein group: 0 [ +0.1s, 2.7s elapsed, 56.6 MB used ]
       +-- read.pgroups_v3: Assigning labels ... [ +0.3s, 2.9s elapsed, 57.4 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_1'. [ 3.1s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_3'. [ 3.2s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_4'. [ +0.1s, 3.3s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_5'. [ 3.3s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_6'. [ 3.4s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_7'. [ 3.5s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_8'. [ 3.6s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_10'. [ 3.7s elapsed, 57.6 MB used ]
          +-- read.pgroups_v3: Assigned label 'Cat_9'. [ 3.8s elapsed, 57.6 MB used ]
       +-- read.pgroups_v3: Generating ID Venn data ... [ +0.3s, 4.2s elapsed, 58.2 MB used ]
       +-- read.pgroups_v3: Standarizing data format ... [ 4.3s elapsed, 58.4 MB used ]
Using 'n' as value column. Use 'value.var' to override
Using 'maxI' as value column. Use 'value.var' to override
       +-- read.pgroups_v3: Filtered out 144 proteins which were not identified in at least 2 biological replicate(s) with at least a total of 2 peptide(s) [ +4.2s, 8.5s elapsed, 59.6 MB used ]
       +-- read.pgroups_v3: Generating quant Venn data ... [ 8.6s elapsed, 59.5 MB used ]
       +-- read.pgroups_v3: Quantifiable proteins: 739 (AFCat1) [ 8.7s elapsed, 58.2 MB used ]
    +-- Performing the analysis ... [ 8.8s elapsed, 36.8 MB used ]
       +-- Preparing limma input data frame ... [ 8.8s elapsed, 36.8 MB used ]
       +-- Saving limma input frame ... [ 8.9s elapsed, 36.9 MB used ]
       +-- Performing quantile normalisation ... [ +0.2s, 9.1s elapsed, 37.8 MB used ]
       +-- Constructing the design matrix ... [ 9.1s elapsed, 38.3 MB used ]
       +-- Fitting the model ... [ 9.2s elapsed, 38.6 MB used ]
Loading required package: MASS
       +-- Constructing the contrast matrix ... [ +0.8s, 10.0s elapsed, 39.7 MB used ]
       +-- Performing hypothesis testing ... [ 10.0s elapsed, 39.7 MB used ]
       +-- Saving analysis results to file ... [ +2.9s, 12.9s elapsed, 41.4 MB used ]
       +-- Generating analysis plots ... [ +0.2s, 13.2s elapsed, 41.5 MB used ]
          +-- Preparing data ... [ 13.2s elapsed, 41.5 MB used ]
          +-- Filtering data based on P-value(s) ... [ +0.1s, 13.3s elapsed, 42.6 MB used ]
          +-- Calculating data frame-row statistics ... [ 13.4s elapsed, 42.6 MB used ]
          +-- Performing final formatting operations ... [ +2.3s, 15.7s elapsed, 44.3 MB used ]
          +-- Plotting time ... [ 15.8s elapsed, 44.3 MB used ]
          +-- Generating plots for combination # 1  ... [ +0.2s, 16.0s elapsed, 44.6 MB used ]
             +-- Making volcano plot ... [ 16.1s elapsed, 44.6 MB used ]
             +-- Making value-ordered plot ... [ +0.8s, 16.8s elapsed, 47.8 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 19.0s elapsed, 50 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 19.9s elapsed, 50 MB used ]
          +-- Generating plots for combination # 2  ... [ 20.1s elapsed, 50.4 MB used ]
             +-- Making volcano plot ... [ 20.2s elapsed, 50.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 20.9s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 23.1s elapsed, 50.4 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 24.0s elapsed, 50.4 MB used ]
          +-- Generating plots for combination # 3  ... [ 24.3s elapsed, 50.4 MB used ]
             +-- Making volcano plot ... [ 24.3s elapsed, 50.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 25.0s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 27.3s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 28.2s elapsed, 50.5 MB used ]
          +-- Generating plots for combination # 4  ... [ 28.4s elapsed, 50.4 MB used ]
             +-- Making volcano plot ... [ 28.5s elapsed, 50.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 29.2s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 31.4s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 32.3s elapsed, 50.5 MB used ]
          +-- Generating plots for combination # 5  ... [ 32.5s elapsed, 50.5 MB used ]
             +-- Making volcano plot ... [ 32.6s elapsed, 50.5 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 33.3s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 35.5s elapsed, 50.5 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 36.4s elapsed, 50.5 MB used ]
          +-- Generating plots for combination # 6  ... [ 36.6s elapsed, 50.5 MB used ]
             +-- Making volcano plot ... [ 36.7s elapsed, 50.5 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 37.4s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 39.5s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 40.5s elapsed, 50.6 MB used ]
          +-- Generating plots for combination # 7  ... [ 40.7s elapsed, 50.5 MB used ]
             +-- Making volcano plot ... [ 40.7s elapsed, 50.6 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 41.5s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 43.7s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +1.0s, 44.6s elapsed, 50.6 MB used ]
          +-- Generating plots for combination # 8  ... [ 44.8s elapsed, 50.6 MB used ]
             +-- Making volcano plot ... [ 44.9s elapsed, 50.6 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 45.6s elapsed, 50.7 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 47.8s elapsed, 50.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 48.7s elapsed, 50.6 MB used ]
          +-- Generating plots for combination # 9  ... [ 48.9s elapsed, 50.6 MB used ]
             +-- Making volcano plot ... [ 49.0s elapsed, 50.6 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 49.7s elapsed, 50.7 MB used ]
Warning: Removed 1 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 1 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.1s, 51.8s elapsed, 50.7 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 52.8s elapsed, 50.7 MB used ]
          +-- Generating plots for combination # 10  ... [ 53.0s elapsed, 50.7 MB used ]
             +-- Making volcano plot ... [ 53.1s elapsed, 50.7 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 53.8s elapsed, 50.7 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 56.0s elapsed, 50.7 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 56.9s elapsed, 50.7 MB used ]
          +-- Generating plots for combination # 11  ... [ 57.1s elapsed, 50.7 MB used ]
             +-- Making volcano plot ... [ 57.2s elapsed, 50.7 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 57.9s elapsed, 50.8 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 60.1s elapsed, 50.7 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 61.0s elapsed, 50.7 MB used ]
          +-- Generating plots for combination # 12  ... [ 61.2s elapsed, 50.7 MB used ]
             +-- Making volcano plot ... [ 61.3s elapsed, 50.7 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 62.0s elapsed, 50.8 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 64.2s elapsed, 50.8 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +1.0s, 65.1s elapsed, 50.8 MB used ]
          +-- Generating plots for combination # 13  ... [ 65.3s elapsed, 50.8 MB used ]
             +-- Making volcano plot ... [ 65.4s elapsed, 50.8 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 66.1s elapsed, 50.8 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 68.3s elapsed, 50.8 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 69.2s elapsed, 50.8 MB used ]
          +-- Generating plots for combination # 14  ... [ 69.5s elapsed, 50.8 MB used ]
             +-- Making volcano plot ... [ 69.5s elapsed, 50.8 MB used ]
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 70.3s elapsed, 50.9 MB used ]
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 13 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 13 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.1s, 72.4s elapsed, 50.9 MB used ]
Warning: Removed 8 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 8 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 73.3s elapsed, 50.8 MB used ]
Warning in cor(x, y, use = "pairwise") : the standard deviation is zero
Warning in cor(x, y, use = "pairwise") : the standard deviation is zero
          +-- Generating plots for combination # 15  ... [ 73.5s elapsed, 50.8 MB used ]
             +-- Making volcano plot ... [ 73.5s elapsed, 50.8 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 74.3s elapsed, 50.9 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 76.4s elapsed, 50.9 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 77.3s elapsed, 50.9 MB used ]
          +-- Generating plots for combination # 16  ... [ 77.6s elapsed, 50.9 MB used ]
             +-- Making volcano plot ... [ 77.6s elapsed, 50.9 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 78.4s elapsed, 50.9 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 80.5s elapsed, 50.9 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 81.4s elapsed, 50.9 MB used ]
          +-- Generating plots for combination # 17  ... [ 81.6s elapsed, 50.9 MB used ]
             +-- Making volcano plot ... [ 81.7s elapsed, 50.9 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 82.4s elapsed, 51 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.2s, 84.6s elapsed, 51 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 1 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 85.6s elapsed, 51 MB used ]
          +-- Generating plots for combination # 18  ... [ 85.8s elapsed, 50.9 MB used ]
             +-- Making volcano plot ... [ 85.8s elapsed, 50.9 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 86.6s elapsed, 51 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.2s, 88.7s elapsed, 51 MB used ]
Warning: Removed 1 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 1 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 89.7s elapsed, 51 MB used ]
          +-- Generating plots for combination # 19  ... [ 89.9s elapsed, 51 MB used ]
             +-- Making volcano plot ... [ 89.9s elapsed, 51 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 90.7s elapsed, 51.1 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.1s, 92.8s elapsed, 51 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 4 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 93.7s elapsed, 51 MB used ]
          +-- Generating plots for combination # 20  ... [ 93.9s elapsed, 51 MB used ]
             +-- Making volcano plot ... [ 94.0s elapsed, 51 MB used ]
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 94.7s elapsed, 51.1 MB used ]
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.2s, 96.9s elapsed, 51.1 MB used ]
Warning: Removed 2 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 2 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 97.9s elapsed, 51.1 MB used ]
          +-- Generating plots for combination # 21  ... [ 98.1s elapsed, 51 MB used ]
             +-- Making volcano plot ... [ 98.1s elapsed, 51 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
             +-- Making value-ordered plot ... [ +0.7s, 98.9s elapsed, 51.1 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_errorbar).
Saving 10 x 7 in image
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_errorbar).
             +-- Making MA plot ... [ +2.1s, 101.0s elapsed, 51.1 MB used ]
Warning: Removed 4 rows containing missing values (geom_point).
Saving 10 x 7 in image
Warning: Removed 4 rows containing missing values (geom_point).
             +-- Making reproducibility plot ... [ +0.9s, 102.0s elapsed, 51.1 MB used ]
          +-- Generating plots for combination # 22  ... [ 102.2s elapsed, 51.1 MB used ]
             +-- Making volcano plot ... [ 102.2s elapsed, 51.1 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 103.0s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 105.1s elapsed, 51.1 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 106.1s elapsed, 51.1 MB used ]
          +-- Generating plots for combination # 23  ... [ 106.3s elapsed, 51.1 MB used ]
             +-- Making volcano plot ... [ 106.3s elapsed, 51.1 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 107.1s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 109.3s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +1.0s, 110.2s elapsed, 51.2 MB used ]
          +-- Generating plots for combination # 24  ... [ 110.4s elapsed, 51.1 MB used ]
             +-- Making volcano plot ... [ 110.5s elapsed, 51.2 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 111.2s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 113.3s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 114.3s elapsed, 51.2 MB used ]
          +-- Generating plots for combination # 25  ... [ 114.5s elapsed, 51.2 MB used ]
             +-- Making volcano plot ... [ 114.5s elapsed, 51.2 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 115.3s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 117.4s elapsed, 51.2 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 118.4s elapsed, 51.2 MB used ]
          +-- Generating plots for combination # 26  ... [ 118.6s elapsed, 51.2 MB used ]
             +-- Making volcano plot ... [ 118.6s elapsed, 51.2 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 119.4s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 121.6s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 122.5s elapsed, 51.3 MB used ]
          +-- Generating plots for combination # 27  ... [ 122.7s elapsed, 51.3 MB used ]
             +-- Making volcano plot ... [ 122.8s elapsed, 51.3 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 123.5s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 125.7s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +1.0s, 126.6s elapsed, 51.3 MB used ]
          +-- Generating plots for combination # 28  ... [ 126.8s elapsed, 51.3 MB used ]
             +-- Making volcano plot ... [ 126.9s elapsed, 51.3 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 127.6s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 129.7s elapsed, 51.3 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 130.7s elapsed, 51.3 MB used ]
          +-- Generating plots for combination # 29  ... [ 130.9s elapsed, 51.3 MB used ]
             +-- Making volcano plot ... [ 130.9s elapsed, 51.3 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 131.7s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 133.9s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 134.8s elapsed, 51.4 MB used ]
          +-- Generating plots for combination # 30  ... [ 135.0s elapsed, 51.4 MB used ]
             +-- Making volcano plot ... [ 135.1s elapsed, 51.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 135.8s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 138.0s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 138.9s elapsed, 51.4 MB used ]
          +-- Generating plots for combination # 31  ... [ 139.1s elapsed, 51.4 MB used ]
             +-- Making volcano plot ... [ 139.2s elapsed, 51.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 139.9s elapsed, 51.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 142.0s elapsed, 51.4 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 143.0s elapsed, 51.4 MB used ]
          +-- Generating plots for combination # 32  ... [ 143.2s elapsed, 51.4 MB used ]
             +-- Making volcano plot ... [ 143.3s elapsed, 51.4 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 144.0s elapsed, 51.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 146.2s elapsed, 51.5 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +1.0s, 147.2s elapsed, 51.5 MB used ]
          +-- Generating plots for combination # 33  ... [ 147.4s elapsed, 51.5 MB used ]
             +-- Making volcano plot ... [ 147.4s elapsed, 51.5 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 148.2s elapsed, 51.5 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 150.3s elapsed, 51.5 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 151.3s elapsed, 51.5 MB used ]
          +-- Generating plots for combination # 34  ... [ 151.5s elapsed, 51.5 MB used ]
             +-- Making volcano plot ... [ 151.6s elapsed, 51.5 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 152.3s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 154.4s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 155.4s elapsed, 51.5 MB used ]
          +-- Generating plots for combination # 35  ... [ 155.6s elapsed, 51.5 MB used ]
             +-- Making volcano plot ... [ 155.7s elapsed, 51.5 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 156.4s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.2s, 158.6s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 159.5s elapsed, 51.6 MB used ]
          +-- Generating plots for combination # 36  ... [ 159.7s elapsed, 51.6 MB used ]
             +-- Making volcano plot ... [ 159.8s elapsed, 51.6 MB used ]
             +-- Making value-ordered plot ... [ +0.7s, 160.5s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making MA plot ... [ +2.1s, 162.7s elapsed, 51.6 MB used ]
Saving 10 x 7 in image
             +-- Making reproducibility plot ... [ +0.9s, 163.6s elapsed, 51.6 MB used ]
          +-- Saving plots results to files ... [ 163.8s elapsed, 51.6 MB used ]
          +-- do_results_plots: Quantified proteins: 739 (AFCat1) [ 163.9s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_3 vs Cat_1 : 385 [ 164.0s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_4 vs Cat_1 : 425 [ 164.0s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_5 vs Cat_1 : 355 [ 164.1s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_6 vs Cat_1 : 381 [ 164.2s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_7 vs Cat_1 : 403 [ 164.2s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_1 : 368 [ 164.3s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_1 : 439 [ 164.3s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_1 : 376 [ 164.4s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_4 vs Cat_3 : 391 [ 164.5s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_5 vs Cat_3 : 378 [ 164.5s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_6 vs Cat_3 : 360 [ 164.6s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_7 vs Cat_3 : 379 [ 164.7s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_3 : 367 [ 164.7s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_3 : 437 [ 164.8s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_3 : 384 [ 164.8s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_5 vs Cat_4 : 435 [ 164.9s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_6 vs Cat_4 : 392 [ 165.0s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_7 vs Cat_4 : 428 [ 165.0s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_4 : 412 [ 165.1s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_4 : 440 [ 165.1s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_4 : 418 [ 165.2s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_6 vs Cat_5 : 327 [ 165.3s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_7 vs Cat_5 : 411 [ 165.3s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_5 : 365 [ 165.4s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_5 : 351 [ 165.4s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_5 : 378 [ 165.5s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_7 vs Cat_6 : 383 [ 165.6s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_6 : 362 [ 165.6s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_6 : 392 [ 165.7s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_6 : 381 [ 165.7s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_8 vs Cat_7 : 394 [ 165.8s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_7 : 374 [ 165.9s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_7 : 391 [ 165.9s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_10 vs Cat_8 : 423 [ 166.0s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_8 : 97 [ 166.1s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed for Cat_9 vs Cat_10 : 419 [ 166.1s elapsed, 51.6 MB used ]
          +-- do_results_plots: Differentially expressed in at least one combination of conditions: 522 [ 166.2s elapsed, 51.6 MB used ]
    +-- Data analysis finished. [ 166.8s elapsed, 53.1 MB used ]
[1] TRUE
> proc.time()
   user  system elapsed 
169.130   0.328 169.445 
