Last active
September 21, 2015 18:46
-
-
Save markrobinsonuzh/da426606d78c99f09eba to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Initial problem posed at: | |
# http://stats.stackexchange.com/questions/173450/an-impossible-estimation-problem?stw=2 | |
set.seed(167) | |
x = rnbinom(100, size=3.2, prob=.8); | |
#x = rnbinom(100, size=3.2, mu=.8); | |
# note: mu = size*(1-prob)/prob .. | |
# in this case, mu=prob (3.2*.2/.8 = .8) | |
n <- 100 | |
ns <- 1000 | |
# randomly create another 999 samples with this setting | |
z <- matrix(nrow=ns,ncol=n) | |
for(i in 2:ns) | |
z[i,] <- rnbinom(n, size=3.2, mu=.8) | |
z[1,] <- x | |
library(edgeR) | |
library(matrixStats) | |
# estimate with edgeR i.e., adjusted profile likelihood w/ no moderation | |
d <- DGEList(z) | |
d$samples$lib.size <- 1 | |
d <- estimateCommonDisp(d) | |
d <- estimateTagwiseDisp(d,prior.df=0) | |
# plot the estimates with the truth (blue), Guillaume's sample (red) | |
plot( 2^f$coefficients, 1/d$tagwise.dispersion, log="y", ylab="size", xlab="mu") | |
abline(v=.8, col="blue", lwd=3) | |
abline(h=3.2, col="blue", lwd=3) | |
points( 2^f$coefficients[1], 1/d$tagwise.dispersion[1], pch=19, cex=2, col="red") | |
# dispersion is basically zero (or size is large) whenever | |
# variance is less than mean | |
#> table( var_lt_mean=rowVars(z) < rowMeans(z), | |
# size_gt_199=1/d$tagwise.dispersion > 199) | |
# size_gt_199 | |
#var_lt_mean FALSE TRUE | |
# FALSE 871 4 | |
# TRUE 0 125 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment