我想用 4 個水平測量 1 因子 ANOVA：ctl反對schiz, bp, dep。我期望aov.run回傳一個帶有 3 個變數的數字向量，因為我正在ctl與其他三個級別進行比較。但是，我只在aov.run. 為什么？
d <- read.table("filtered.mds", header=T)
ann <- read.table("clinical_table.txt", header=T, sep="\t")
# Create new dataframe
dat <- t(cbind(d$C1,d$C2))
colnames(dat) <- paste(ann$Profile, data.table::rowid(ann$Profile), sep="_")
rownames(dat) <- c("C1", "C2")
# Levels
ctl <- grepl("^Unaffected control", ann$Profile)
schiz <- grepl("^Schiz.", ann$Profile)
bp <- grepl("^BP", ann$Profile)
dep <- grepl("^Dep.", ann$Profile)
# 1-factor ANOVA with 4 levels
aov.lvl <- function(x,s1,s2,s3,s4) {
x1 <- as.numeric(x[s1])
x2 <- as.numeric(x[s2])
x3 <- as.numeric(x[s3])
x4 <- as.numeric(x[s4])
fac <- c(rep("A",length(x1)), rep("B",length(x2)), rep("C",length(x3)), rep("D",length(x4)))
a.dat <- data.frame(as.factor(fac),c(x1,x2,x3,x4))
names(a.dat) <- c("factor","express")
p.out <- summary(aov(express~factor, a.dat))[[1]][1,5]
return(p.out)
}
aov.run <- apply(dat, 1, aov.lvl, s1=ctl, s2=schiz, s3=bp, s4=dep)
資料框d
> dput(d)
structure(list(FID = c("AC10", "AC11", "AC12", "AC13", "AC14",
"AC15", "AC17", "AC18", "AC19", "AC1", "AC20", "AC21", "AC22",
"AC23", "AC24", "AC25", "AC26", "AC27", "AC29", "AC2", "AC30",
"AC31", "AC32", "AC33", "AC34", "AC35", "AC36", "AC37", "AC38",
"AC39", "AC3", "AC40", "AC41", "AC42", "AC43", "AC45", "AC46",
"AC47", "AC48", "AC49", "AC50", "AC51", "AC52", "AC53", "AC54",
"AC55", "AC56", "AC57", "AC58", "AC5", "AC60", "AC61", "AC62",
"AC63", "AC64", "AC65", "AC66", "AC67", "AC69", "AC6", "AC70",
"AC71", "AC72", "AC73", "AC74", "AC75", "AC76", "AC77", "AC78",
"AC79", "AC7", "AC80", "AC81", "AC82", "AC83", "AC84", "AC86",
"AC87", "AC88", "AC89", "AC8", "AC90", "AC91", "AC92", "AC9",
"AC100", "AC101", "AC102", "AC103", "AC104", "AC105", "AC16",
"AC68", "AC93", "AC94", "AC95", "AC96", "AC97", "AC99", "DE10",
"DE12", "DE13", "DE14", "DE15", "DE16", "DE17", "DE18", "DE19",
"DE1", "DE20", "DE21", "DE22", "DE23", "DE25", "DE26", "DE27",
"DE2", "DE33", "DE34", "DE35", "DE36", "DE37", "DE38", "DE39",
"DE3", "DE40", "DE41", "DE42", "DE44", "DE45", "DE46", "DE47",
"DE48", "DE49", "DE4", "DE50", "DE51", "DE52", "DE53", "DE54",
"DE55", "DE56", "DE57", "DE58", "DE59", "DE60", "DE7", "DE9",
"DE29", "DE30", "DE32", "DE43", "DE5"), IID = c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L), SOL = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L), C1 = c(-0.00385609, 0.0101138, -0.0146168, -0.0218236, -0.0134745,
-0.017089, 0.0152448, 0.0134359, 0.00540102, -0.0125389, 0.00463956,
-0.00416079, -0.000325898, 0.0132781, 0.0130666, 0.00718399,
-0.0051912, -0.0227934, 0.0364974, -0.0180301, -0.0226556, -0.00585266,
0.0258924, -0.00994298, -0.00380612, 0.0187883, 0.0103367, 0.00747272,
0.0191431, -0.00501846, -0.00118336, 0.0361201, 0.00830498, 0.00380194,
0.00667686, -0.000441697, -0.00170991, -0.0281008, -0.00424591,
0.0213412, 0.00261405, 0.016154, 0.0098956, 0.0141544, 0.0367203,
0.0144693, 0.0256731, -0.00218851, 0.0204603, -0.000603019, -0.00504176,
-0.00917368, 0.00237875, 0.0175946, 0.0188388, 0.0368965, -0.00408476,
0.00871812, -0.00851917, 0.0252035, -0.00915532, 0.0223745, 0.016866,
0.026825, 0.0366276, 0.0540474, 0.0386237, 0.0029996, 0.0207176,
0.0177353, -0.0066377, 0.0343811, 0.0282509, 0.00526683, 0.0459516,
0.00976286, 0.0259005, -0.00104822, -0.012696, 0.0134071, 0.0231658,
0.00359455, 0.0194968, -0.000936478, -0.0029218, -0.0058512,
-0.000837274, -0.0129465, -0.0102079, -0.00559039, 0.0118966,
0.00147658, 0.0120396, -0.0104779, -0.0315149, -0.0115454, -0.0122457,
-6.72242e-05, 0.00370599, -0.0164126, -0.0107853, -0.0271741,
-0.0212005, -0.0445118, -0.0387773, -0.025109, -0.0321735, -0.0398603,
-0.0266408, -0.0260984, -0.0296337, -0.0185381, -0.0403944, 0.0197937,
-0.0176322, -0.013238, -0.0071666, -7.27277e-05, 0.00397489,
0.0335056, -0.00604706, -0.00926438, 0.00706601, -0.0156982,
-0.0275085, -0.00864179, -0.0247967, -0.030564, -0.00767327,
-0.0235161, 0.00649758, -0.0329062, -0.0016138, -0.00701695,
0.00819454, 0.0100377, 0.0250199, -0.0493141, -0.0216641, -0.0244709,
-0.00466616, 0.016751, -0.0191688, -0.00492488, -0.0162364, -0.0167085,
-0.0113427, 0.000422333, 0.030274, 0.0317995, 0.00237194, -0.00693838,
-0.0100835), C2 = c(0.000865365, -0.001752, 0.0189917, -0.023343,
-0.0340531, -0.0258976, -0.00794043, 0.0173163, 0.00639341, -0.0343077,
0.01083, -0.0402179, 0.0158751, -0.00262893, -0.0216757, -0.00261259,
-0.00542089, -0.00515714, 0.0105216, -0.0193606, 0.00692795,
-0.0117295, -0.0235627, -0.00850041, -0.0156109, -0.00871875,
-0.0163218, 0.0227143, -0.0161961, -0.0176719, -0.0070994, 0.0262932,
0.00164033, -0.00969917, -0.0197631, -0.0154387, -0.0194608,
0.00442207, -0.0234804, 0.00822342, -0.00657274, -0.0092332,
0.0130892, -0.0345162, -0.0114187, -0.0129497, -0.00306092, 0.0417858,
0.0262002, -0.0188849, -0.0184154, -0.0109956, -0.0151195, -0.00414531,
0.010064, 0.0308816, -0.0153337, 0.0157867, -0.0289866, -0.0106713,
0.000112714, -0.00152177, 0.0184509, 0.0112357, 0.00097954, 0.032083,
0.0190258, -0.0371498, -0.0307498, -0.00947645, -0.00198995,
0.015845, -0.0240248, -0.0122369, -0.00107049, -0.0144661, 0.0207883,
-0.0418619, -0.0123712, -0.0212721, -0.00667244, -0.028512, -0.00522357,
-0.018842, -0.0123026, -0.00511655, 0.0188473, 0.00739189, 0.0321578,
-0.015449, 0.0214631, -0.00995001, -0.00144645, 0.00934907, 0.0344757,
-0.0220224, 0.0121403, -0.00615057, -0.0208969, 0.0313899, -0.0251011,
0.011635, 0.00536455, 0.0233033, -0.0019204, 0.0273593, 0.00844028,
0.00181444, 0.02824, 0.0255231, 0.00266055, -0.00850383, -0.0129938,
0.0268634, 0.0195986, 0.0320615, -0.0026514, 0.0127147, 0.014279,
0.0553434, -0.020963, 0.00629119, -0.0244099, -0.0080923, 0.0173508,
0.0485753, -0.00666049, 0.0501603, 0.0029162, 0.0267363, 0.0066606,
0.00857736, 0.0172693, -0.00827586, -0.0117478, -0.00336638,
0.00954265, -0.00889617, 0.00290055, 0.0229832, 0.0504569, 0.025979,
-0.00795356, -0.0135421, -0.00359528, 0.0150037, -0.0105817,
0.0167827, 0.0110882, 0.00200862, -0.00597284, -0.0188371, -0.00827599
)), class = "data.frame", row.names = c(NA, -153L))
柱子ann$Profile
> dput(ann$Profile)
c("Schiz.", "Schiz.", "Schiz.", "BP", "BP", "Unaffected control",
"Schiz.", "BP", "Unaffected control", "BP", "BP", "BP", "Schiz.",
"BP", "Unaffected control", "Schiz.", "Schiz.", "Unaffected control",
"Unaffected control", "BP", "Unaffected control", "Schiz.", "BP",
"Unaffected control", "BP", "Unaffected control", "BP", "Schiz.",
"Unaffected control", "Schiz.", "Schiz.", "Schiz.", "Schiz.",
"BP", "Unaffected control", "Schiz.", "BP", "Schiz.", "BP", "Unaffected control",
"BP", "Unaffected control", "Unaffected control", "Unaffected control",
"Unaffected control", "Schiz.", "Unaffected control", "BP", "BP",
"BP", "Unaffected control", "BP", "BP", "BP", "BP", "Unaffected control",
"Schiz.", "Unaffected control", "BP", "BP", "Unaffected control",
"Unaffected control", "BP", "Schiz.", "BP", "Schiz.", "BP", "Unaffected control",
"Schiz.", "Unaffected control", "Schiz.", "Unaffected control",
"Schiz.", "Schiz.", "Unaffected control", "Unaffected control",
"Unaffected control", "Schiz.", "Schiz.", "BP", "BP", "Unaffected control",
"Unaffected control", "Schiz.", "Schiz.", "Schiz.", "Schiz.",
"BP", "Unaffected control", "BP", "Unaffected control", "BP",
"Schiz.", "Schiz.", "Schiz.", "Unaffected control", "Unaffected control",
"Schiz.", "Unaffected control", "Unaffected control", "Unaffected control",
"BP", "BP", "Dep.", "Unaffected control", "Unaffected control",
"Dep.", "Dep.", "Dep.", "Dep.", "Dep.", "Unaffected control",
"Unaffected control", "Schiz.", "Dep.", "BP", "Dep.", "Schiz.",
"Schiz.", "Schiz.", "BP", "Unaffected control", "Unaffected control",
"Unaffected control", "BP", "BP", "Dep.", "Schiz.", "Dep.", "BP",
"Unaffected control", "Unaffected control", "Schiz.", "Schiz.",
"Unaffected control", "Unaffected control", "BP", "BP", "Schiz.",
"Dep.", "BP", "Dep.", "BP", "Schiz.", "Unaffected control", "Dep.",
"BP", "Schiz.", "Dep.", "Dep.", "BP", "BP", "Schiz.")
uj5u.com熱心網友回復：
aov.run正在回傳與分別在每個列上運行的 ANOVA 關聯的 p 值。每個 ANOVA 只有一個 p 值，因此 C1 有一個，C2 有一個，總共有兩個。這按預期作業！
聽起來您對通過 Tukey 測驗或類似方法獲得的 ANOVA 的事后結果感興趣。Tukey 的 HSD 將分別為您提供每個比較的 p 值，每個 ANOVA 進行 6 次比較（“Dep.-BP”、“Schiz.-BP”、“Unaffected control-BP”、“Schiz.-Dep.”、“Unaffected” control-Dep.”和“Unaffected control-Schiz.”），聽起來您只對“Unaffected control-BP”、“Unaffected control-Dep.”和“Unaffected control-Schiz”感興趣。比較。您可以通過將呼叫替換summary()為tukeyHSD()：
v <- cbind(d, Profile=ann$Profile)
# p-value for each ANOVA
summary(aov(C1~Profile, data = v))[[1]][1,5]
summary(aov(C2~Profile, data = v))[[1]][1,5]
# p-value for each comparison within the ANOVA
TukeyHSD(aov(C1~Profile, data = v))
TukeyHSD(aov(C2~Profile, data = v))
轉載請註明出處，本文鏈接：https://www.uj5u.com/ruanti/445269.html