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I want to sort the matrix where all the summary statistics are stored by p-value.

Code

library(nlme)

# Sort the matrix where all the summary statistics are stored by p-value
for (i in 1:nrow(p)){
  p.a.sort <- sort(rep(r$Class, nrow(p[i,])))
  p.b.sort <- c(sort(rep(1:sum(r$Class==0), nrow(p[i,]))), sort(rep(1:sum(r$Class==1), nrow(p[i,]))))
  p.c.sort <- rep(1:nrow(p[i,]), ncol(p[i,]))
}

pmx <- data.frame(colnames(p), p.a.sort, p.b.sort, p.c.sort)
for (j in colnames(p)){
  lmx <- lme(j~p.a.sort*p.c.sort,pmx,random=~1|p.b.sort)
}
out <- anova(summary(lmx))

Traceback

Error in eval(predvars, data, env) : object 'JHU_113_2.CEL' not found

Data snippet

> dput(p[1:3,1:3])
structure(list(JHU_113_2.CEL = c(0.09655, 0.64864, 0.0073), JHU_144.CEL = c(0.04224, 
0.38068, 0.00293), JHU_173.CEL = c(0.22314, 0.49589, 0.03034)), row.names = c(2315252L, 
2315253L, 2315374L), class = "data.frame")

> dput(r[1:3,])
structure(list(Class = c(1, 0, 1), Results = c("JHU_113_2.CEL", 
"JHU_144.CEL", "JHU_173.CEL")), row.names = c(NA, 3L), class = "data.frame")
melolili
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