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I tried to use random forest to classify microarray data. Basing on research of L.Breiman and Tao Shi, I constructed a synthetic data base using bootstrap methods (Assuming it is a matrix with samples on row and genes on column, for each gene in each sample, values are selected with replacement in the gene column, descripted in http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm#unsup ).

The original data is labeled as 1, and the synthetic data is labeled as 2. The combined data is used as input for random forest as supervised data. The wired stuff is that I got a error rate of 100%. In my view, the worst case would be the error is 50%, which means randomly participate the combined dataset. I tried this approach for many times, it always gave nearly 100% error rate.

In practical, my data set is 7*297 matrix, 7 samples and 297 genes.

Besides, I have a problem in understanding how unsupervised pattern work in the R "randomForest" package, and how it calculate the proximity. From the source code, I get this:

if (!is.null(y)) {
    if (length(y) != n) 
        stop("length of response must be the same as predictors")
    addclass <- FALSE
}
else {
    if (!addclass) 
        addclass <- TRUE
    y <- factor(c(rep(1, n), rep(2, n)))
    x <- rbind(x, x)
}

It seems that the new data set is treated as combined raw data. However, I didn't get observed result if the assumption is true:

iris.urf <- randomForest(iris[, -5])
iris.urf$proximity[1:5,1:5]
MDSplot(iris.urf, iris$Species)

xx.1 <- randomForest(as.matrix(rbind(iris[, -5],iris[, -5])),factor(rep(1:2,each=150)),proximity=TRUE)
xx.1$proximity[1:5,1:5]
xx.2 <- xx.1$proximity
xx.1$proximity <- xx.2[1:150,1:150]
MDSplot(xx.1, iris$Species)

The proximity is very different, but the mdsplot gives similar pattern.

Could someone help me on these?

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1  
This usually happens when you have paradoxes in the data, i.e. pairs of identical samples with respect to genes and with different classes. However I don't understand why are you doing this -- unsupervised model is not a very useful construct, in practice it is only good for clustering objects (i.e. samples in your case). – mbq♦ Sep 3 '12 at 17:11
With 7 observations there's probably not enough data points. A random forest is an ensemble of trees, and trees typically require more data points to learn the classification model – JCWong Sep 3 '12 at 17:11
@mbq: I do want to use proximity produced by RF to cluster samples. Another advantage of RF is that it also provide importance for each variable, which will be helpful in selecting subset variable for downstream analysis. – hiberbear Sep 4 '12 at 8:44
1  
@hiberbear Well, clustering 7 samples... but it is doable. But importance certainly won't make any sense here. Let's say those are all human genes -- thus you'll get genes responsible for eye color, arthritis and alcohol tolerance mixed together. Without decision, how the forest can tell which gene set to look for? This way you will only get some random selection depending on how datum objects were generated. – mbq♦ Sep 4 '12 at 8:58
1  
@hiberb This is becouse you don't bootstrap your variables in class 2. This procedure is described in the page you have cited and is implemented in the function createClass which is located in the source file rfutils.c (line 25) and createClass itself is called from classRF (line 238, file rf.c). – O_Devinyak Sep 7 '12 at 16:54
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