我有一个包含25个耐药株和25个敏感株系的代谢物数据集。数据如下所示，每一列都是一行，每一行都是代谢物：
> dput(head(df,20))
structure(list(Metabolites = structure(1:20,.Label = c("M001","M002","M003","M004","M005","M006","M007","M008","M009","M010","M011","M012","M013","M014","M015","M016","M017","M018","M019","M020","M021","M022","M023","M024","M025","M026","M027","M028","M029","M030","M031","M032","M033","M034","M035","M036","M037","M038","M039","M040","M041","M042","M043","M044","M045","M046","M047","M048","M049","M050","M051","M052","M053","M054","M055","M056","M057","M058","M059","M060","M061","M062","M063","M064","M065","M066","M067","M068","M069","M070","M071","M072","M073","M074","M075","M076","M077","M078","M079","M080","M081","M082","M083","M084","M085","M086","M087","M088","M089","M090","M091","M092","M093","M094","M095","M096","M097","M098","M099","M100","M101","M102","M103","M104","M105","M106","M107","M108","M109","M110","M111","M112","M113","M114","M115","M116","M117","M118","M119","M120","M121","M122","M123","M124","M125","M126","M127","M128","M129","M130","M131","M132","M133","M134","M135","M136","M137","M138","M139","M140","M141","M142","M143","M144","M145","M146","M147","M148","M149","M150","M151","M152","M153","M154","M155","M156","M157","M158","M159","M160","M161","M162","M163","M164","M165","M166","M167","M168","M169","M170","M171","M172","M173","M174","M175","M176","M177","M178","M179","M180","M181","M182","M183","M184","M185","M186","M187","M188","M189","M190","M191","M192","M193","M194","M195","M196","M197","M198","M199","M200","M201","M202","M203","M204","M205","M206","M207","M208","M209","M210","M211","M212","M213","M214","M215","M216","M217","M218","M219","M220","M221","M222","M223","M224","M225","M226","M227","M228","M229","M230","M231","M232","M233","M234","M235","M236","M237","M238","M239","M240","M241","M242","M243","M244","M245","M246","M247","M248","M249","M250","M251","M252","M253","M254","M255","M256","M257","M258","M259","M260","M261","M262","M263","M264","M265","M266","M267","M268","M269","M270","M271","M272","M273","M274","M275","M276","M277","M278","M279","M280","M281","M282","M283","M284","M285","M286","M287","M288","M289","M290","M291","M292","M293","M294","M295","M296","M297","M298","M299","M300","M301","M302","M303","M304","M305","M306","M307","M308","M309","M310","M311","M312","M313","M314","M315","M316","M317","M318","M319","M320","M321","M322","M323","M324","M325","M326","M327","M328","M329","M330","M331","M332","M333","M334","M335","M336","M337","M338","M339","M340","M341","M342","M343","M344","M345","M346","M347","M348","M349","M350","M351","M352","M353","M354","M355","M356","M357","M358","M359","M360","M361","M362","M363","M364","M365","M366","M367","M368","M369","M370","M371","M372","M373","M374","M375","M376","M377","M378","M379","M380","M381","M382","M383","M384","M385","M386","M387","M388","M389","M390","M391","M392","M393","M394","M395","M396","M397","M398","M399","M400","M401","M402","M403","M404","M405","M406","M407","M408","M409","M410","M411","M412","M413","M414","M415","M416","M417","M418","M419","M420","M421","M422","M423","M424","M425","M426","M427","M428","M429","M430","M431","M432","M433","M434","M435","M436","M437","M438","M439","M440","M441","M442","M443","M444","M445","M446","M447","M448","M449","M450","M451","M452","M453","M454","M455","M456","M457","M458","M459","M460","M461","M462","M463","M464","M465","M466","M467","M468","M469","M470","M471","M472","M473","M474","M475","M476","M477","M478","M479","M480","M481","M482","M483","M484","M485","M486","M487","M488","M489","M490","M491","M492","M493","M494","M495","M496","M497","M498","M499","M500","M501","M502","M503","M504","M505","M506","M507","M508","M509","M510","M511","M512","M513","M514","M515","M516","M517","M518","M519","M520","M521","M522","M523","M524","M525","M526","M527","M528","M529","M530","M531","M532","M533","M534"),class = "factor"),R =
c(-0.368417113,-0.101138639,-0.161723188,0.202453574,-0.255021436,0.990889582,-0.14527723,0.079853308,0.029544276,0.441221431,-0.11944612,-0.305230969,0.03355256,1.03727535,0.320838857,0.057860187,-0.220164171,-2.526670332,-0.367387096,0.802085235),R.1 = c(0.335923239,3.061811172,-0.035662198,-0.607682577,0.777607579,-0.058005603,1.137154667,1.023908735,0.028284344,-0.044308897,-0.411500613,1.399836977,0.439845793,2.247067657,-0.742871026,1.568088682,0.11575394,5.04122684,2.374395515,1.541474963),R.2 = c(-0.005240453,-0.298993563,-0.033124556,0.000437247,-0.363018191,0.326128083,0.21257698,-0.205006227,-0.091374353,-0.370715168,-0.267458783,0.248780422,1.630503285,1.874717025,0.069540933,-0.436639754,0.133565845,-2.078394913,0.540959939,-0.190331212),R.3 = c(0.02178722,0.571957417,0.00324566,-0.061805284,0.162608704,-0.325539348,-0.053329502,0.227249242,-0.025090981,-0.080247253,0.144508557,-0.088720932,1.263644554,0.996155965,0.210446023,1.990889582,0.076457177,4.421971981,0.198741153,-0.855116946),R.4 = c(0.006111685,0.021758841,-0.00737953,0.380875266,-0.276248724,-0.011315313,-0.107602955,-0.104603974,0.343158603,-0.457723898,-0.03562391,0.193219285,-0.063940821,0.149473244,-0.019274012,-0.676331271,0.512558704,-0.994071688,0.059564554,1.429864917),R.5 = c(0.166168642,0.037674433,0.086877451,-0.231273643,0.221108542,-0.186011986,-0.089551585,-0.061788592,-0.018223759,0.071986113,0.101146723,-0.049779048,-0.518114903,1.253322095,0.216780998,0.165038055,-0.439934372,0.382512734,0.421213338,1.001105937),R.6 = c(-0.232768963,-0.261850899,-0.142152384,-0.342128282,-0.207394664,0.031122517,-0.088355874,-0.324414618,0.083484986,-0.381236261,-0.11649968,0.124415109,0.358689609,1.043033998,0.038236206,-0.996719549,-0.01579871,-1.273254248,0.551507204,0.900665975),R.7 = c(-0.121204957,-0.269377573,0.025763096,-0.370846136,0.288406834,0.110607324,-0.076961982,-0.629167859,-0.265012055,-0.505201609,-0.023481433,-0.17856392,0.865332323,0.524969082,-0.291204505,0.719516623,-0.012732085,-1.941620399,0.663526717,1.199444088),R.8 = c(-0.141327295,0.152181413,0.153037654,-0.097868883,-0.191620073,0.259454516,0.583256179,-0.772155023,0.272534699,0.814200162,0.248763352,0.315661336,1.902073579,3.385926093,0.53062173,0.309248961,0.006293118,-2.517164686,0.301678975,0.353796149),R.9 = c(-0.384312139,0.06505404,-0.073435447,-0.715351781,0.217991274,-0.304059998,-0.102759574,0.231438468,-0.403444624,0.294886468,-0.085702486,-0.480999914,-0.433684562,0.7205518,0.005892568,0.731183242,-0.290235435,1.642113301,1.033423002,0.404841732),R.10 = c(0.043284098,-0.187714919,0.103755766,0.494175476,0.183367264,0.048461489,0.341167603,0.942935915,0.231005552,-0.032843257,0.110780431,0.369394834,1.09200937,1.745564723,0.411796215,0.852997588,0.335184192,-0.440708907,0.203262185,1.007914836),R.11 = c(0.083099508,0.267121498,0.015533879,-0.144656445,-0.101470878,0.222392421,-0.266252913,0.890823438,-0.210945895,-0.848512247,-0.067114196,-0.25944549,0.221455302,0.806681407,-0.042501067,0.260151897,-0.040791883,-1.787941649,0.382274808,0.938294929),R.12 =
c(-0.705217235,2.542562534,-0.135227381,-0.443646178,0.519586492,0.043795118,0.686317021,1.041588324,-0.304393436,-0.234275413,-0.43566302,1.195857383,1.752478594,1.497997192,-0.80811711,1.677544508,0.208963846,3.621611552,2.73039294,0.799138017),R.13 = c(0.42312992,0.183353267,0.147085025,-0.266112283,0.324924347,0.183090771,0.20325984,-0.250088093,-0.24489442,0.005137198,-0.116409492,0.03395771,1.37097252,1.869706252,0.235820911,1.090602549,-0.225066556,1.028663758,0.590223864,-0.134533181),R.14 = c(0.048153022,0.279512674,-0.015087144,0.345647904,-0.066420426,-0.099863894,0.002270174,0.663318138,-0.13597767,0.122096476,-0.020838519,0.128906398,-0.620454804,2.291401419,0.112474729,0.093509451,0.211284031,0.57905586,0.319030146,-0.748749321),R.15 = c(-0.019510824,0.115344305,0.004854839,-0.57797607,0.242971645,-0.085664592,-0.186912355,0.411476387,-0.173219579,-0.575194724,-0.184830499,-0.066941159,-0.832648942,2.396326768,-0.120558924,1.286370872,0.137328874,-0.415249645,-0.123145792,0.396469739),R.16 =
c(0.123458788,0.237039197,0.092887298,-0.079751022,0.056754778,-0.445799753,0.013420516,0.100152869,0.119695066,-0.15320627,0.009168315,-0.17625064,-0.029486765,1.666907682,0.276289737,1.188035155,0.046047368,0.280843392,0.542246519,0.847685006),R.17 = c(0.108754902,0.020919096,-0.122974045,-0.280708392,-0.288840707,0.084474568,-0.295709099,-0.398888114,-0.644341048,-0.775756783,-0.548916159,-0.180266946,-0.564083771,1.007945835,-0.250767066,0.229068486,-0.272062897,0.545069774,-0.590980007,0.286389802),R.18 =
c(-0.819717423,0.946193556,-0.096635783,-0.397640449,-0.404948682,-0.005217709,0.361129545,1.449898022,0.076338824,-0.689502486,-0.437063806,0.886017472,0.837525303,1.192266964,-1.132614108,-3.602036014,0.368129605,-3.349106876,1.454669286,1.465455406),R.19 = c(0.620445088,-0.415932471,0.112894056,-0.15182218,0.174272257,0.111202562,-0.840963315,-1.107727456,0.105602182,-0.255257055,0.280560458,-1.043602781,-0.090670359,1.593968549,1.352097575,0.586873898,-0.219566377,-0.725140159,0.324350757,1.013175389),R.20 =
c(0.245063967,0.113375519,0.092986888,0.288600861,-0.02038524,0.004543925,0.190331212,-0.199632058,0.018920862,0.130545468,0.138523024,0.984010269,1.984278002,0.042850965,0.983598393,0.098937541,0.548928809,0.083001425,-0.042997405),R.21 = c(0.661566826,0.119437254,0.091438651,-0.715355635,0.061747686,-0.744882623,-0.024626971,0.12485642,-0.591404712,-0.368052144,-0.195621484,-0.112050968,1.025425329,0.453802053,-0.254558205,0.155103041,-0.045724139,-0.266813345,0.513923164,0.730513197),R.22 = c(0.34075977,0.290896243,0.099535674,0.0828218,0.081235304,0.139222747,-0.0077634,0.336721484,-0.055014102,-0.174725988,0.016240641,-0.10410469,-1.439586959,1.326737974,-0.078921802,-0.053470209,0.154328146,0.149227196,0.418521645,-0.324534591),R.23 =
c(-0.007948753,0.17967325,0.015206413,-0.127001855,-0.094574813,0.334241356,0.124851487,0.128964093,-0.031364171,-0.467678979,0.001269419,-0.010840947,-0.265703593,1.368883853,-0.116494992,-0.392426988,0.063286245,0.067375329,0.338763899,1.268311492),R.24 = c(-0.206450877,-0.277674691,-0.049784833,0.227339641,0.077055427,0.454548402,0.26706616,0.102023049,0.016301812,0.518421645,0.032254199,0.117301336,1.246234735,1.851766791,0.151897009,0.120904889,-0.091315167,-2.760725806,0.960369191,1.034626343),S = c(0.402177532,0.420055574,0.176453044,0.198545679,0.697700712,0.257629601,0.041820176,1.020353532,-0.208399149,0.137707165,0.201996393,0.048339534,-0.707179047,2.282832351,0.028758993,1.288589164,-0.078759733,-0.186109073,0.344746177,-0.552074207),S.1 =
c(1.203313446,0.466087228,0.587909785,0.849665727,0.927068478,0.900155762,0.666443903,0.587368998,0.707134371,0.583025997,-0.00695835,0.577717726,0.725546578,1.901779685,-0.21032333,0.319245674,0.109198771,-1.136286206,-0.647850963,0.374345671),S.2 =
c(-0.875181736,0.65620627,-0.028983688,-0.135730534,0.358207527,-0.15277028,-0.067694407,-0.55682075,-0.056583528,0.738471539,0.104744105,-0.62940378,0.028515371,1.857176942,0.533757723,0.450724355,-0.312065883,-0.176636838,0.457017571,0.9536772),S.3 = c(0.588257773,-0.004822383,0.053954091,0.084236537,0.460311579,0.125835216,0.096404484,-0.355126928,0.21176328,0.234658286,-0.27556876,0.415037499,1.357233048,1.305564649,-0.465708593,1.262304112,0.110473998,1.171660703,0.415336783,0.837677625),S.4 = c(0.741814035,4.425151813,0.16639331,0.078002512,1.210404071,0.470250842,1.341152662,1.190877372,0.329602023,1.182913983,0.023918627,1.744449024,0.894972523,3.493155756,-0.620596763,2.040804149,0.236774856,2.586085658,2.247754539,-0.254284144),S.5 = c(0,0.007502765,-0.028720823,0.004278881,-1.099986727,0.15926652,-0.047631122,-0.020210187,0.229170954,0.115369782,0.131861561,-0.307095488,0.137154667,2.853523128,0.329790213,1.451427879,0.056204602,-1.178436104,0.217307132,-0.13196534),S.6 = c(-0.097674532,0.204931451,-0.051225323,-0.113849077,-0.304976169,-0.218640286,0.068503564,-0.112268983,0.115141225,-0.075998876,0.101573667,0.053061244,2.147169087,1.947962735,-0.03231389,0.932885804,0.342297684,-2.342396544,-0.179376477,0.47767359),S.7 = c(0.478736427,0.097003889,0.096215315,0.45495651,0.050843677,0.106915204,0.087578298,0.140944127,0.052787414,-0.027338709,0.124964208,0.270931736,-0.178294391,1.769631783,0.078304995,0.471482646,0.272772601,-1.593511279,0.386425363,0.0138058),S.8 = c(-0.156557778,0.044163331,-0.010018756,-0.144204723,-0.032552115,-0.639055204,0.187733306,0.272767852,-0.118499236,0.153039566,-0.023246344,-0.01053836,0.438884241,1.547487795,0.290668675,-0.294716135,-0.171756995,-4.196230266,0.155476957,1.36156786),S.9 = c(0.03088456,0.026459045,0.026537138,0.280405137,-0.151398317,-0.285216317,-0.085020584,-0.227058321,0.037186602,-0.157265791,0.163116612,0.242552369,-0.185978979,2.27217506,-0.03099791,1.119271892,0.010281641,-0.858385395,0.680822516,0.869603363),S.10 =
c(-0.933612603,-0.561661401,-0.010971118,0.084506296,0.327996931,-0.127379306,0.372832796,-0.496799668,0.306224012,0.774497651,-0.016301812,0.118511278,1.584962501,1.104115103,0.371968777,0.84789681,-0.422532036,-0.165301976,0.360402243,1.316057507),S.11 =
c(0.158086968,-0.16276126,0.058752587,0.334639147,-0.236693103,0.19592021,0.189362494,-0.170716666,0.412125904,-0.186556808,0.019746348,0.513638785,0.979906429,0.711042249,-0.196017653,1.536277987,0.278880442,0.2421449,-0.140854662,-0.892002748),S.12 = c(-0.103349527,0.008171537,0.00740795,0.230358731,0.008814865,0.059265949,0.256748143,-0.029081064,0.058693994,0.245492585,-0.046478319,-0.272943002,0.266249071,0.438993478,0.214384273,0.174833802,-0.107021711,0.025829916,0.547141035,-0.018962311),S.13 =
c(0.098720989,0.087518126,-0.036205038,-0.096469371,0.154284035,0.144596821,0.03090228,0.137503524,-0.100928909,-0.111945526,-0.099622711,-0.060255248,-0.3379805,1.422995021,0.06065222,0.439371453,-0.038819249,-1.051399153,-0.190932002,-0.564482695),S.14 =
c(0.181128626,0.048144347,0.082784875,0.164744762,-0.192795853,0.679907305,-0.013862653,0.446737964,-0.340500201,-0.063834709,-0.039999772,-0.476580935,1.429061666,0.043243186,0.96893928,0.027823682,-1.492793697,0.316419333,0.409292824),S.15 = c(0.038395379,0.001808342,0.119825623,0.175174518,0.030871971,0.976623217,0.131155431,0.157773076,0.265868136,0.180653687,0.240570256,1.327638515,2.925137937,0.09894185,1.495915625,0.236760712,-1.783214151,1.440123224,-1.006173287),S.16 = c(0.26489715,0.618994392,0.119147265,0.428553572,-0.112110366,-0.053977621,0.152664728,-0.740156602,0.121136438,0.074861437,-0.037941572,0.025671408,2.236333895,0.212915143,0.991816796,0.226770862,-2.156734325,-0.168712606,0.53196331),S.17 = c(0.195724471,0.004644926,0.055255112,0.160263427,0.020340448,0.36325156,0.180808289,0.010481859,0.086611107,0.071709873,0.119690699,0.180955701,0.64309333,3.040632365,0.243708653,1.188487452,0.141495436,1.260289029,0.635859213,0.152117679),S.18 = c(-0.209778803,-0.194816177,-0.06734922,-0.157660246,-0.322157988,-0.085877835,-0.164075926,0.322299716,-0.145776183,-0.044931851,0.10228105,0.049327712,1.003411973,1.339959808,0.104617003,0.650394253,-0.03789984,-3.153164235,0.831164535,0.715554624),S.19 = c(0.121624202,0.227489373,0.129994473,0.185885669,0.013160365,0.054966459,0.067986838,0.266339551,0.123382416,0.075101455,0.180398333,0.355694209,0.178705887,1.356842621,-0.14448904,-0.343652866,0.32081973,-0.410169692,1.146938038,0.791776524),S.20 = c(-0.078601215,0.831950488,0.058102955,-0.486632366,0.507899167,-0.036069255,0.508578267,0.725146477,-0.648288436,0.047828525,-0.39820306,0.663167328,0.688127986,2.014873276,-1.228761946,1.194816177,0.037371429,-0.00250093,2.610433188,0.941635837),S.21 = c(-0.658223681,0.514305072,0.071083098,-0.535674538,0.508087425,-0.118021974,0.031406847,-0.220352916,-0.327403225,0.059973955,-0.142100162,-0.283264771,-0.295316365,1.163403665,0.085747948,-0.622437206,-0.283547003,-3.427114726,0.503542524,-0.194592393),S.22 =
c(0.502575109,0.214738849,0.16387432,-1.058339765,0.314335635,0.400198512,-0.134555177,0.525833289,-0.471621028,-0.19065835,-0.096404484,-0.250315154,-2.200389125,1.296830599,-0.194787667,0.704871964,0.100567477,-1.596585726,-0.285145107,0.873242858),S.23 =
c(-0.60259496,-0.301673433,-0.116609187,0.255225081,-0.263307928,-0.124370693,0.174581628,-0.232733207,0.190477241,0.380540255,-0.074136422,0.087765536,1.566966071,1.595043184,0.05055783,0.612866668,-0.19426882,-0.358166123,0.577028319,0.528832273),S.24 = c(0.041270996,-0.129181684,-0.059588796,-0.003285788,-0.175620198,0.422784607,-0.068934631,0.059378547,0.03562391,-0.034765418,-0.068083945,0.065987814,-0.291090691,1.771431998,0.046542586,-0.876278566,0.276660352,-4.220478101,-0.018334524,0.793037619)),row.names = c(NA,20L),class = "data.frame")
我想找到在抗性和易感品系之间显示出显着差异的代谢物。谁能指导我如何在R中做到这一点？
我不知道该怎么做，所以我首先将两组中的每25条线平均成两个数据列，然后使用以下代码在#R中使用#limma软件包进行检查：
Group <- factor(c("R","S"))
design <- model.matrix(~0 + Group)
colnames(design) <- gsub("Group","",colnames(design))
fit <- lmFit(dset[,2:3],design)
contrast.matrix<-makeContrasts(RvsS=R-S,levels=design)
fit2<-contrasts.fit(fit,contrast.matrix)
fit2<-eBayes(fit2)
sel.diif<-p.adjust(fit2$F.p.value,method="fdr")<0.05
deg<-eset[,2:3][sel.diif,]
它给出了以下错误：
Error in .ebayes(fit = fit,proportion = proportion,stdev.coef.lim = stdev.coef.lim,: No residual degrees of freedom in linear model fits