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Summarization

Shiying Xiao1^1, Charles Watt1^1, Jennifer C. Liddle2^2, Jeremy L. Balsbaugh2^2, Timothy E. Moore3^3

1^1Department of Statistics, UConn
2^2Proteomics and Metabolomics Facility, UConn
3^3Statistical Consulting Services, UConn

2025-06-11

Source: vignettes/summarization.Rmd
summarization.Rmd

Preliminary 

## load R package
library(msDiaLogue)
## preprocessing
fileName <- "../tests/testData/Toy_Spectronaut_Data.csv"
dataSet <- preprocessing(fileName,
                         filterNaN = TRUE, filterUnique = 2,
                         replaceBlank = TRUE, saveRm = TRUE)
## transformation
dataTran <- transform(dataSet, logFold = 2)
## normalization
dataNorm <- normalize(dataTran, normalizeType = "quant")
## imputation
dataImput <- impute.min_local(dataNorm, reportImputing = FALSE,
                              reqPercentPresent = 0.51)
## filtering
dataImput <- filterNA(dataImput, saveRm = TRUE)

Example 

dataSumm <- summarize(dataImput, saveSumm = TRUE)
Condition Stat NUD4B_HUMAN A0A7P0T808_HUMAN A0A8I5KU53_HUMAN ZN840_HUMAN CC85C_HUMAN C9JEV0_HUMAN C9JNU9_HUMAN ALBU_BOVIN CYC_BOVIN TRFE_BOVIN F8W0H2_HUMAN H0Y7V7_HUMAN H0YD14_HUMAN H3BUF6_HUMAN H7C1W4_HUMAN H7C3M7_HUMAN TLR3_HUMAN LRIG2_HUMAN RAB3D_HUMAN ADH1_YEAST LYSC_CHICK BGAL_ECOLI CYTA_HUMAN KPCB_HUMAN LIPL_HUMAN CO6_HUMAN BGAL_HUMAN SYTC_HUMAN CASPE_HUMAN DCAF6_HUMAN DALD3_HUMAN HGNAT_HUMAN RFFL_HUMAN RN185_HUMAN ZN462_HUMAN ALKB7_HUMAN POLK_HUMAN ACAD8_HUMAN
100pmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.00000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
100pmol mean 10.6532858 12.0862074 10.6232407 8.2644365 8.8486965 6.8764321 8.1789684 16.75777 13.0941802 14.0233390 9.0659703 10.0672927 9.9408634 7.9781022 7.8297313 9.8230915 7.4096023 8.5986327 10.0905795 15.1604531 13.6952175 14.3757288 8.8924636 9.8735187 8.2974346 6.7681823 11.7142153 14.7560796 6.3848929 7.9228836 9.6214990 10.6043210 7.0043419 10.0418355 8.6778910 6.8092287 7.8188307 7.5025180
100pmol sd 0.5083417 0.6509735 0.5994044 0.2816079 0.1066916 0.8168644 0.3116711 0.00000 0.3622393 0.1193272 0.0851570 0.1210474 0.3098987 0.1768750 0.2999079 0.4757395 0.3381959 0.1721820 0.1134697 0.0051583 0.1891971 0.1167288 0.1962332 0.2378070 0.1527627 0.2813447 0.4244383 0.0084914 0.5214944 0.3804140 0.5609915 0.3619004 0.1950282 0.2935700 0.4716454 0.5391294 1.0406244 0.0733600
100pmol median 10.4407055 11.9866645 10.9044011 8.3357977 8.8600566 6.8358159 8.0231329 16.75777 12.9649865 13.9738814 9.0817277 10.0484610 10.0134747 7.9517960 7.6845225 9.7242975 7.4036982 8.5641998 10.0759323 15.1630323 13.6276559 14.4308715 8.8615327 9.8954204 8.2462263 6.7711653 11.7430198 14.7603253 6.2126514 7.9250089 9.7619876 10.6813371 7.0054690 10.0348410 8.4713152 7.0555925 7.3283898 7.5303791
100pmol trimmed 10.6532858 12.0862074 10.6232407 8.2644365 8.8486965 6.8764321 8.1789684 16.75777 13.0941802 14.0233390 9.0659703 10.0672927 9.9408634 7.9781022 7.8297313 9.8230915 7.4096023 8.5986327 10.0905795 15.1604531 13.6952175 14.3757288 8.8924636 9.8735187 8.2974346 6.7681823 11.7142153 14.7560796 6.3848929 7.9228836 9.6214990 10.6043210 7.0043419 10.0418355 8.6778910 6.8092287 7.8188307 7.5025180
100pmol mad 0.1376914 0.4989033 0.0779088 0.1770303 0.0972461 0.9173216 0.0000000 0.00000 0.1081516 0.0217987 0.0808661 0.0801917 0.1879022 0.1813007 0.0204763 0.3690956 0.3054035 0.1314032 0.1116108 0.0000000 0.0563232 0.0136146 0.1880212 0.2347672 0.0740280 0.2559629 0.4989033 0.0000000 0.3084771 0.4747480 0.3554415 0.2043118 0.1783076 0.3469740 0.1169605 0.0886895 0.1125840 0.0185508
100pmol min 10.3252183 11.4065141 9.7272105 7.8681709 8.7105178 6.0045864 8.0231329 16.75777 12.8190919 13.9444754 8.9641549 9.9402840 9.5045393 7.8295103 7.6707114 9.3765069 7.0015026 8.4331596 9.9784883 15.1527157 13.5516770 14.2011179 8.7105178 9.5741849 8.1793065 6.4207163 11.2912962 14.7433424 6.0045864 7.5303791 8.8329716 10.0976598 6.7643932 9.7272105 8.3924265 6.0045864 7.2420363 7.3939101
100pmol max 11.4065141 12.9649865 10.9569499 8.5179795 8.9641549 7.8295103 8.6464751 16.75777 13.6276559 14.2011179 9.1362711 10.2319649 10.2319649 8.1793065 8.2791689 10.4672641 7.8295103 8.8329716 10.2319649 15.1630323 13.9738814 14.4400544 9.1362711 10.1290492 8.5179795 7.1096825 12.0795254 14.7603253 7.1096825 8.3111376 10.1290492 10.9569499 7.2420363 10.3704495 9.3765069 7.1211431 9.3765069 7.5554037
100pmol range 1.0812958 1.5584724 1.2297394 0.6498087 0.2536371 1.8249239 0.6233422 0.00000 0.8085640 0.2566425 0.1721162 0.2916809 0.7274256 0.3497962 0.6084576 1.0907573 0.8280077 0.3998121 0.2534766 0.0103166 0.4222044 0.2389365 0.4257533 0.5548643 0.3386730 0.6889662 0.7882292 0.0169829 1.1050961 0.7807586 1.2960775 0.8592901 0.4776431 0.6432390 0.9840804 1.1165567 2.1344706 0.1614936
100pmol skew 0.6975575 0.3239948 -0.7349674 -0.4906058 -0.2153643 0.0746172 0.7500000 NaN 0.6663690 0.7189584 -0.1695960 0.3387430 -0.4796405 0.1114972 0.7458050 0.3783514 0.0392202 0.3827303 0.1991275 -0.7500000 0.6668586 -0.7378644 0.2135796 -0.1711657 0.5944647 -0.0238336 -0.0237842 -0.7500000 0.4773224 -0.0050802 -0.4861771 -0.4499095 -0.0129955 0.0322210 0.6966507 -0.7281063 0.7407580 -0.6901803
100pmol kurtosis -1.7260359 -1.8707238 -1.6982833 -1.8448761 -1.9494341 -2.1798795 -1.6875000 NaN -1.7327385 -1.7058522 -2.2461322 -1.8404530 -1.8192490 -2.3106519 -1.6904097 -1.9467364 -1.8757984 -1.9169430 -2.1242147 -1.6875000 -1.7325055 -1.6961436 -2.1614305 -2.0285590 -1.8014680 -1.8757000 -2.4101207 -1.6875000 -1.9257747 -2.3455313 -1.8463172 -1.8132208 -1.8755701 -2.2325877 -1.7280983 -1.7033814 -1.6940017 -1.7210573
100pmol se 0.2541708 0.3254868 0.2997022 0.1408039 0.0533458 0.4084322 0.1558356 0.00000 0.1811196 0.0596636 0.0425785 0.0605237 0.1549494 0.0884375 0.1499539 0.2378698 0.1690980 0.0860910 0.0567349 0.0025791 0.0945985 0.0583644 0.0981166 0.1189035 0.0763814 0.1406723 0.2122191 0.0042457 0.2607472 0.1902070 0.2804957 0.1809502 0.0975141 0.1467850 0.2358227 0.2695647 0.5203122 0.0366800
200pmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.00000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
200pmol mean 10.6488941 9.9995022 11.2485095 8.4505628 8.2445037 6.7465842 8.3091726 16.75777 13.2471248 13.7426617 9.2570565 10.1413903 9.9978891 8.0880583 7.5631150 10.0415877 7.5210813 8.4008606 10.2414149 15.1516556 14.1141044 14.7415973 8.8133014 10.1732192 8.4520910 7.0971425 12.1775775 14.4198014 6.1065048 7.4951113 9.9165721 10.5958169 6.7744045 9.4079382 8.8671576 7.5851679 7.2449244 8.1196440
200pmol sd 0.3289432 1.9911564 0.8373275 0.1881608 0.7094445 0.3664652 0.2468009 0.00000 0.6260180 0.2671713 0.2010541 0.1943193 0.2312942 0.2050339 0.5491845 0.0887966 0.1270932 0.1803556 0.2480010 0.0244819 0.1612898 0.0403015 0.3108902 0.2385763 0.2290557 0.1059008 0.7605739 0.0435834 0.2038367 0.2849943 0.2242693 0.9901032 0.2858241 0.5064716 0.2453451 0.5268763 0.1931332 0.7646020
200pmol median 10.6304571 9.7995222 11.1621879 8.3564824 8.3484718 6.7376547 8.2084906 16.75777 13.2458280 13.7905186 9.2558074 10.0987350 9.9817300 8.1461655 7.7353428 10.0234743 7.5323272 8.3648486 10.2534127 15.1516556 14.1765162 14.7415973 8.7218404 10.1940134 8.3863145 7.0862137 12.0450654 14.4198014 6.0045864 7.5577355 9.9522318 10.8173322 6.7514941 9.5814615 8.9536853 7.7794486 7.2650103 8.1324727
200pmol trimmed 10.6488941 9.9995022 11.2485095 8.4505628 8.2445037 6.7465842 8.3091726 16.75777 13.2471248 13.7426617 9.2570565 10.1413903 9.9978891 8.0880583 7.5631150 10.0415877 7.5210813 8.4008606 10.2414149 15.1516556 14.1141044 14.7415973 8.8133014 10.1732192 8.4520910 7.0971425 12.1775775 14.4198014 6.1065048 7.4951113 9.9165721 10.5958169 6.7744045 9.4079382 8.8671576 7.5851679 7.2449244 8.1196440
200pmol mad 0.3347575 2.1765166 0.8761545 0.0000000 0.6980566 0.4553758 0.0870596 0.00000 0.6618078 0.2237764 0.1806811 0.1226153 0.2710782 0.0924032 0.3469760 0.0606518 0.1398648 0.1655239 0.2242486 0.0314340 0.0679752 0.0517460 0.2144922 0.2723765 0.0986746 0.1126230 0.7255181 0.0559598 0.0000000 0.1924863 0.2172056 0.7118132 0.2244197 0.2182024 0.1292411 0.1544898 0.1731190 0.9350762
200pmol min 10.2776193 8.1425613 10.4132587 8.3564824 7.3752661 6.4122599 8.1497697 16.75777 12.4949559 13.3877224 9.0120719 9.9548324 9.7988903 7.7926907 6.8071641 9.9548324 7.3752661 8.2532043 9.9271211 15.1304537 13.8810204 14.7066952 8.5771674 9.9271211 8.2532043 6.9939476 11.5162454 14.3820570 6.0045864 7.0987676 9.6415866 9.2323577 6.4487561 8.6699394 8.5204024 6.8071641 6.9939476 7.3078254
200pmol max 11.0570429 12.2564034 12.2564034 8.7328039 8.9058051 7.0987676 8.6699394 16.75777 14.0018871 14.0018871 9.5045393 10.4132587 10.2292060 8.2672115 7.9746103 10.1645698 7.6444045 8.6205408 10.5317133 15.1728576 14.2223649 14.7764995 9.2323577 10.3777288 8.7825308 7.2221951 13.1039337 14.4575457 6.4122599 7.7662064 10.1202381 11.5162454 7.1458739 9.7988903 9.0408573 7.9746103 7.4557295 8.9058051
200pmol range 0.7794236 4.1138421 1.8431447 0.3763215 1.5305390 0.6865077 0.5201698 0.00000 1.5069312 0.6141647 0.4924674 0.4584263 0.4303157 0.4745208 1.1674462 0.2097374 0.2691384 0.3673366 0.6045922 0.0424039 0.3413445 0.0698043 0.6551903 0.4506077 0.5293266 0.2282475 1.5876883 0.0754887 0.4076734 0.6674389 0.4786515 2.2838877 0.6971178 1.1289508 0.5204548 1.1674462 0.4617819 1.5979797
200pmol skew 0.1104304 0.0985966 0.1459698 0.7500000 -0.1912656 0.0093515 0.6449274 NaN 0.0043414 -0.3241272 0.0139784 0.4541046 0.0251965 -0.5691072 -0.4497921 0.4200330 -0.1005912 0.1958428 -0.1071276 0.0000000 -0.6030234 0.0000000 0.3944221 -0.0390722 0.5750774 0.1306423 0.1932636 0.0000000 0.7500000 -0.4413140 -0.1975122 -0.4230438 0.1788057 -0.6265175 -0.5283584 -0.6785550 -0.2152922 -0.0172273
200pmol kurtosis -1.9967978 -2.3005634 -2.1833090 -1.6875000 -2.1856515 -2.4193545 -1.7713239 NaN -1.9494170 -1.9815481 -1.8749421 -1.8267257 -2.4085003 -1.7742906 -1.9525773 -1.8484890 -2.2706637 -2.2173611 -1.8856612 -2.4375000 -1.8081396 -2.4375000 -2.0080976 -2.3926118 -1.7717059 -2.2279404 -2.2134019 -2.4375000 -1.6875000 -1.8538031 -2.1927634 -1.9000912 -1.8654864 -1.7689149 -1.8768601 -1.7272841 -1.9293663 -2.3195181
200pmol se 0.1644716 0.9955782 0.4186638 0.0940804 0.3547223 0.1832326 0.1234004 0.00000 0.3130090 0.1335856 0.1005271 0.0971597 0.1156471 0.1025170 0.2745923 0.0443983 0.0635466 0.0901778 0.1240005 0.0122409 0.0806449 0.0201508 0.1554451 0.1192882 0.1145278 0.0529504 0.3802869 0.0217917 0.1019184 0.1424971 0.1121346 0.4950516 0.1429120 0.2532358 0.1226726 0.2634382 0.0965666 0.3823010
50pmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.00000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
50pmol mean 11.0652499 7.8125342 9.9553033 7.9185075 8.6105032 8.4512816 8.3913880 16.75777 12.6233713 13.9262822 9.6052951 9.6068208 10.3568778 8.5314736 6.9189678 9.8860972 7.1716461 8.6447744 10.4687736 14.6152277 13.4461368 14.2433512 10.2782600 10.2093348 8.6777501 7.2864883 11.7603897 15.1244369 8.3934284 7.6429483 8.6746639 9.8868633 6.7178161 9.3454998 8.2512331 7.9571364 6.6190600 6.8997407
50pmol sd 0.3708294 2.1115541 1.4597325 0.9959061 0.2809902 0.8229885 0.3063097 0.00000 0.5173426 0.1372130 0.1226801 0.3575152 0.1220664 0.0795662 0.6676726 0.1165080 0.1981263 0.3160745 0.0959664 0.1699854 0.2963109 0.1601637 0.5386107 0.0229454 0.3383377 0.3091468 0.4929381 0.0069476 1.0544361 0.3132572 0.6136998 0.5930033 0.3291763 0.4604039 1.2832479 0.7029085 0.7121212 0.1642577
50pmol median 10.9683118 7.6184720 10.6629030 8.2827405 8.7328039 8.1702259 8.4708099 16.75777 12.4001796 13.8638704 9.5814615 9.4721898 10.3777288 8.5378538 7.0311799 9.8910321 7.0975242 8.5250934 10.5071517 14.6967905 13.3228123 14.2433512 10.0613581 10.2093348 8.6563070 7.2411414 11.5354444 15.1244369 7.9908823 7.6231715 8.4093360 10.1031519 6.6331386 9.3019021 8.5967555 7.8149531 6.5819142 6.8229624
50pmol trimmed 11.0652499 7.8125342 9.9553033 7.9185075 8.6105032 8.4512816 8.3913880 16.75777 12.6233713 13.9262822 9.6052951 9.6068208 10.3568778 8.5314736 6.9189678 9.8860972 7.1716461 8.6447744 10.4687736 14.6152277 13.4461368 14.2433512 10.2782600 10.2093348 8.6777501 7.2864883 11.7603897 15.1244369 8.3934284 7.6429483 8.6746639 9.8868633 6.7178161 9.3454998 8.2512331 7.9571364 6.6190600 6.8997407
50pmol mad 0.1772529 2.3927468 0.0491467 0.2910204 0.0392287 0.2849493 0.2027294 0.00000 0.1405153 0.0254266 0.1140448 0.1623808 0.0777336 0.0742326 0.4317120 0.1344530 0.0915028 0.1415103 0.0364151 0.0146847 0.0962357 0.2056452 0.1292707 0.0294612 0.4002908 0.3181482 0.0885564 0.0089205 0.2820706 0.3397979 0.1646671 0.1801448 0.2580102 0.4729686 0.8120600 0.6061193 0.8559462 0.0117113
50pmol min 10.7292010 6.0045864 7.7662064 6.4487561 8.1906821 7.8062907 7.9641396 16.75777 12.3054034 13.8467203 9.5045393 9.3626655 10.1894635 8.4296461 6.0045864 9.7537182 7.0358064 8.4296461 10.3290776 14.3606346 13.2579022 14.1046454 9.9116818 10.1894635 8.3863145 7.0265534 11.4757140 15.1184202 7.6371168 7.3078254 8.2982695 9.0120719 6.4591131 8.8665134 6.4487561 7.3321259 6.0045864 6.8071641
50pmol max 11.5951749 10.0086064 10.7292010 8.6597927 8.7857227 9.6583837 8.6597927 16.75777 13.3877224 14.1306676 9.7537182 10.1202381 10.4825900 8.6205408 7.6089249 10.0086064 7.4557295 9.0992648 10.5317133 14.7066952 13.8810204 14.3820570 11.0786419 10.2292060 9.0120719 7.6371168 12.4949559 15.1304537 9.9548324 8.0176249 9.5817142 10.3290776 7.1458739 9.9116818 9.3626655 8.8665134 7.3078254 7.1458739
50pmol range 0.8659739 4.0040200 2.9629945 2.2110366 0.5950406 1.8520929 0.6956531 0.00000 1.0823190 0.2839473 0.2491788 0.7575726 0.2931265 0.1908947 1.6043385 0.2548883 0.4199231 0.6696188 0.2026357 0.3460606 0.6231181 0.2774116 1.1669601 0.0397425 0.6257574 0.6105634 1.0192419 0.0120335 2.3177155 0.7097995 1.2834446 1.3170057 0.6867608 1.0451685 2.9139094 1.5343875 1.3032390 0.3387098
50pmol skew 0.5345800 0.0433923 -0.7489636 -0.6758677 -0.7319474 0.6482699 -0.4719094 NaN 0.6863654 0.7197869 0.1859854 0.5810642 -0.3693859 -0.1673018 -0.3638798 -0.0569700 0.5757638 0.5855057 -0.6293395 -0.7433054 0.6602470 0.0000000 0.7076234 0.0000000 0.0207596 0.1085464 0.7215694 0.0000000 0.6913135 0.1018067 0.6878480 -0.6741805 0.3120345 0.1554845 -0.4939928 0.2926118 0.0140868 0.7453289
50pmol kurtosis -1.7865070 -2.3876770 -1.6881769 -1.7283357 -1.6985019 -1.7416477 -1.8858332 NaN -1.7364638 -1.7097999 -2.2281384 -1.8279658 -1.8337864 -1.9347058 -1.8350942 -2.2311257 -1.8328016 -1.8239282 -1.7848527 -1.6921905 -1.7582380 -2.4375000 -1.7131106 -2.4375000 -2.4135931 -2.3139585 -1.7084245 -2.4375000 -1.7208848 -2.1366725 -1.7352502 -1.7295690 -2.0930099 -2.1113622 -1.8670313 -2.0889369 -2.4212634 -1.6904792
50pmol se 0.1854147 1.0557771 0.7298663 0.4979530 0.1404951 0.4114942 0.1531548 0.00000 0.2586713 0.0686065 0.0613401 0.1787576 0.0610332 0.0397831 0.3338363 0.0582540 0.0990632 0.1580372 0.0479832 0.0849927 0.1481555 0.0800818 0.2693054 0.0114727 0.1691689 0.1545734 0.2464691 0.0034738 0.5272181 0.1566286 0.3068499 0.2965017 0.1645881 0.2302020 0.6416239 0.3514543 0.3560606 0.0821289

Details

This summarization provides a table of values for each protein in the final dataset that include the final processed abundances and fold changes in each condition, and that protein’s statistical relation to the global dataset in terms of its mean, median, standard deviation, and other parameters.

The column “Stat” in the generated result includes the following statistics:

  • n: Number.
  • mean: Mean.
  • sd: Standard deviation.
  • median: Median.
  • trimmed: Trimmed mean with a trim of 0.1.
  • mad: Median absolute deviation (from the median).
  • min: Minimum.
  • max: Maximum.
  • range: The difference between the maximum and minimum value.
  • skew: Skewness.
  • kurtosis: Kurtosis.
  • se: Standard error.

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