[BioC] Different results with limma on R 1.8.1 and R 1.9.0
Gordon Smyth
smyth at wehi.edu.au
Tue May 25 06:50:22 CEST 2004
The change-log for limma is at
http://bioinf.wehi.edu.au/limma/changelog.txt. I can't think of any changes
which I'd expect to make a difference. If you want to track down the reason
you need to be more proactive yourself, by giving a reproducible example or
at very least identifying which function introduced the difference.
Gordon
>Did something change between versions of Limma for R 1.8.1 and 1.9.0 that I
>missed? Where did the NAs come from? These are the results from running
>topTable on four dye-swapped arrays. My code is identical in both cases.
>
>Thanks, Dave.
>
>Approximate R code (cut and pasted from Java):
>
>RG <- new("RGList", list(R=Rs,G=Gs,Rb=Rbs,Gb=Gbs))
>
>RG$printer <-
>list(ngrid.r=max(genefile$V1),ngrid.c=max(genefile$V2),nspot.r=max(genefile$
>V3),nspot.c=max(genefile$V4))
>
>controlgenes <-
>c("rbcL","LTP4","cab","RCA","XCP2","KLF5","beta-actin","blank")
>
>status <- as.character(genefile$V5 %in% controlgenes)
>
>weights <- modifyWeights(weights,status,values="TRUE",multipliers=0)
>
>MA <- normalizeWithinArrays(RG, method="printtiploess", layout = RG$printer,
>weights=weights)
>
>MA <- normalizeBetweenArrays(MA)
>
>RGnorm <- RG.MA(MA)
>
>fit <- lmFit(MA,design=designmatrix,ndups=3,spacing=3)
>
>eb <- eBayes(fit,proportion=0.01)
>
>topGenes <- topTable(eb,number=30, adjust.method="fdr",genelist=genenb,
>sort.by="B")
>
>
>R 1.8.1 and Limma 1.3.11
>
>AA936757 3.719032040892476 13.29244868974321
>21.273219140535428 1.7700675638573854E-8
>16.41630333165485
>
>AA683077 2.012539960953221 11.482499529443794
>13.663709222466158 2.0625199090952707E-6
>11.250663857920369
>
>R60193 -1.3466735409962498 10.752153167818404
>-13.03136976097657 2.4313326561267002E-6
>10.685625239796412
>
>AA495846 -1.6680548543855949 12.382884989290126
>-12.671686948601973 2.5492658305820254E-6
>10.351882638349387
>
>AA488391 -1.4254635359938195 14.808395517282252
>-10.843395066628524 1.283926471841737E-5
>8.501052463671101
>
>AA487582 -1.228055202475718 11.663677107858677
>-10.178183283163676 2.227968350968346E-5
>7.7559891264874485
>
>AA115076 -0.9539621605022185 12.078999589916572 -9.624781911437797
>3.621290380935091E-5 7.103310688538175
>
>rbcL -0.7072592325606469 15.672906565723503
>-9.374764679536662 4.270881833754837E-5
>6.798070109334531
>
>N92478 0.7189453707342979 12.281634742105913
>8.549326128043308 1.0637336404591882E-4
>5.741441090946004
>
>R43483 1.202633856423655 12.863115098568308
>8.239234808480374 1.35077439495208E-4
>5.324064717014463
>
>W65461 -0.8499390380452945 11.862250529587449
>-8.171524696487337 1.35077439495208E-4
>5.2313772459233325
>
>R22625 1.007519719039666 11.685107805563577
>8.148614344126274 1.35077439495208E-4
>5.199887898229524
>
>N64741 0.7156235702764399 11.809730661346153
>7.870773633988644 1.8158032889909942E-4
>4.812803441820608
>
>cab -1.2941102587414737 15.680695154681269
>-7.595232962116644 2.470103994514213E-4
>4.419245595896798
>
>H99588 0.8652153443867413 11.392510470124181
>7.534377849323958 2.5114113484872455E-4
>4.3310008628463175
>
>AI091770 0.8504457738567389 12.106173602043109
>7.237131332358541 3.600014660391982E-4
>3.8929531152731576
>
>N47099 -0.8114613642578669 12.662883264096203
>-7.138898624042952 3.856946884800288E-4
>3.745596346529296
>
>AA927490 0.8516455736631379 12.848624380999476 7.091226324062262
>3.856946884800288E-4 3.6736147292532495
>
>H93335 0.7766571255106037 11.626933364317638
>7.055574805801781 3.856946884800288E-4
>3.6195822554773978
>
>AA460756 -0.722318285156469 12.914573719569278
>-7.037093214568916 3.856946884800288E-4
>3.5915040918515695
>
>H91651 0.8999563298639041 11.531392574985665
>6.981365473171944 3.988349279240792E-4
>3.5065580814100192
>
>R98064 0.5788079495799782 13.92756842842436
>6.925988294495901 4.022593487966753E-4
>3.4217262940760174
>
>N92519 -0.8817222351213301 12.325915022550825
>-6.8959183292308674 4.022593487966753E-4
>3.3754864306526473
>
>H57309 1.0221437769371449 11.665260456460624
>6.885789182466807 4.022593487966753E-4
>3.3598824729822754
>
>AA676254 0.6331758737992141 12.333616026625913 6.803062369233151
>4.3712786030422087E-4 3.231913465384914
>
>R70685 0.7174146630194426 12.522316848076509
>6.7508474635412545 4.5473122234414076E-4
>3.1506570801542066
>
>AA156324 0.6274341213034178 13.95646992606678 6.709548771767108
>4.6613320948945386E-4 3.0861213173329025
>
>AA970865 0.7372368804313136 12.529532666637065 6.616778943118437
>5.092549091370438E-4 2.940291066618914
>
>AA426311 1.1933268346805304 12.384127923158252 6.604555005565974
>5.092549091370438E-4 2.9209863477282267
>
>AI266752 0.6269423513027547 12.315553383243532
>6.454717305524467 6.20093863325188E-4
>2.682661207506496
>
>
>
>R 1.9.0 and Limma 1.6.2
>
>AA936757 3.719032040892476 10.559981507974102
>28.23882285130472 7.863145275660577E-10 19.413771711320685
>
>H29557 -1.897133224001365 15.350252408436896 -19.413578403894515
>3.988945258694179E-8 15.20366412339247
>
>AA425823 -1.666448034534032 11.02998345932825
>-15.292205566460252 4.790547716180304E-7 12.374499220492003
>
>AA504505 -1.4474488966374865 12.078999589916572
>-14.87358063161449 5.010456645004823E-7 12.042391815850303
>
>R59304 1.544443491508911 11.453083271566156 13.271793476075693
>1.3297285005387517E-6 10.67797369790008
>
>R60193 -1.3466735409962498 10.7521531678184 -13.242098267228087
>1.3297285005387517E-6 10.651167901354318
>
>AA495846 -1.6680548543855949 12.38288498929012
>-12.750002501701173 1.780703847793079E-6 10.19828768873374
>
>AA487582 -1.228055202475718 12.65779688842052
>-12.349291873690223 2.265897629733821E-6 9.816997544388586
>
>H77652 0.9059438434642344 12.256507847750266 9.83023585045215
>2.7275150855477153E-5 7.124830784102192
>
>rbcL -0.7072592325606469 15.6729065657235 -9.751179795203823
>2.7275150855477153E-5 7.031042906997234
>
>N62259 0.7123986545109168 15.049128544130609 9.629646891234945
>2.853790704567304E-5 6.885633360176124
>
>AA404273 -0.9996886769470037 11.43235822647634
>-9.389025706663572 3.198886319749833E-5 6.593265337263933
>
>N59764 -0.7145132049203675 15.676890538969966 -9.36240960883919
>3.198886319749833E-5 6.56055438319232
>
>W92278 -1.1476019449939237 10.439293470618457
>-9.327682420283907 3.198886319749833E-5 6.517762525489527
>
>AA148641 -0.9404721200518092 15.082140123430541
>-8.861667197571945 5.258261946783176E-5 5.930945556384787
>
>N92478 0.7189453707342979 12.281634742105913 8.805175962280739
>5.2876863355363295E-5 5.858183976942382
>
>AI000633 1.6008005679752557 9.955996678736588
>8.180663817805218 1.0879675440219568E-4 5.029306410490687
>
>NA NaN 12.337598516303787 -8.109277965186818
>1.0879675440219568E-4 4.93161742950074
>
>H14569 -1.0380998956395908 11.531392574985661 -8.10822919035774
>1.0879675440219568E-4 4.930177603648442
>
>W96155 -0.572117857511056 14.869545562513855
>-8.01482513126453 1.1280454960831163E-4 4.801407377034307
>
>AI356395 -1.1000763326219425 9.452794366579658
>-8.005509561604235 1.1280454960831163E-4 4.7885059099214935
>
>H98218 0.6001708323940103 13.334379713309595 7.275588365011955
>2.9398547598623775E-4 3.7435867091686763
>
>cab -1.2941102587414737 11.46022414171325 -7.123140520806918
>3.4972921801739885E-4 3.5166308112029494
>
>R43483 1.202633856423655 11.014639250100172 6.857870675428175
>4.933421851847506E-4 3.1143009120476144
>
>NA NaN 10.896076797612105 6.798345329400819
>4.937898133672889E-4 3.022712666695405
>
>AA902249 -0.66593123879359 14.260402317937773
>-6.792525490061204 4.937898133672889E-4 3.0137321220865587
>
>RCA 2.4220685426497868 8.673579100397403 7.006012361156719
>4.937898133672889E-4 2.96802105001
>
>AI337373 0.9378765424156126 11.790798293433005
>6.749319582910434 4.937898133672889E-4 2.9469169513263953
>
>AA952925 -0.8110412337442618 13.950937078203266
>-6.738004595584546 4.937898133672889E-4 2.929376916256361
>
>AA933077 0.48901878798830556 15.501228055330621
>6.726858105944119 4.937898133672889E-4 2.9120809607229425
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