similar to: heatmap.2: question regarding the "raw z-score"

Hi, I would like to run random Forest classification algorithm and check the accuracy of the prediction according to different training and testing schemes. For example, extracting 70% of the samples for training and the rest for testing, or using 10-fold cross validation scheme. How can I do that? Is there a function? Thanks a lot, Chrysanthi. [[alternative HTML version deleted]]

Hi everyone, I have just started using R, and I have a simple question. How can I get the Standard deviation for rows. basically I am looking for something like "rowMeans()" but for Standard deviation (I tried "rowSds()" didn't exist) Thanks, -- View this message in context: http://www.nabble.com/Standard-deviation-for-rows-tp19998106p19998106.html Sent from the R

Hello, I am a phd student in Bioinformatics and I am using the Random Forest package in order to classify my data, but I have some questions. Is there a function in order to visualize the trees, so as to get the rules? Also, could you please provide me with the code of "randomForest" function, as I would like to see how it works. I was wondering if I can get the classification having

Dear all, I am working with randomForest package and I am interested in examining the "Gini importance" measures that are used as a general indicator of feature relevance. Is there a possibility of getting the Gini measure that is being estimated in each tree by the output of the getTree() function? Thanks a lot, Chrysanthi [[alternative HTML version deleted]]

Hi, May be this helps: ?set.seed(24) ?mydata4<- as.data.frame(matrix(sample(1:100,10*38,replace=TRUE),ncol=38)) ?dim(mydata4) #[1] 10 38 ?library(matrixStats) res<-do.call(cbind,lapply(1:400, function(i) {permutation<-sample(mydata4); (rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))} )) ?dim(res) #[1]? 10 400 A.K.

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

Hi people, If there is a fn "colMeans" why isn't there a "colSDs" etc Thanks, Phil. -- Philip Rhoades Pricom Pty Limited (ACN 003 252 275) GPO Box 3411 Sydney NSW 2001 Australia Mobile: +61:0411-185-652 Fax: +61:2:8923-5363 E-mail: pri at chu.com.au -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table("final.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist,

After reading the ZFS docs it does appear that RAID-Z can be used on a two-disk system and I was wondering if the system would [i]basically [/i]work as Intel''s Matrix RAID for two disks? [u] Intel Matrix RAID info:[/u] http://www.intel.com/design/chipsets/matrixstorage_sb.htm http://techreport.com/reviews/2005q1/matrix-raid/index.x?pg=1 My focus with this thread is some

Hi everyone, I have dataset which I make a sample of it couple of times and each time I get the mean and standard deviation of each row for each sample. I have a function for that, which takes the name of the file and number of times to sample and then returns the mean and standard deviation for each row in each sample. Sample=function(name, n){

Dear R Help list, My question is regarding extracting the standard error or Z-score from a cph or coxph call. My Cox model is: - modz=cph(Surv(TSURV,STATUS)~RAGE+DAGE+REG_WTIME_M+CLD_ISCH+POLY_VS, data=kidneyT,method="breslow", x=T, y=T) I've used names(modz) but can't see anything that will let me extract the Z scores for each coefficient or the standard errors in the same

Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package is checked. For instance, currently I get: * using log directory

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

Dear friends i am trying to fit an Ornstein-Uhlenbeck process by MAXIMUM LIKELYHOOD method. i found these formulas on http://www.sitmo.com/article/calibrating-the-ornstein-uhlenbeck-model/ this is the mean-reverting process http://r.789695.n4.nabble.com/file/n4637271/process.txt process.txt and this is the script that i am using....... ouFit.ML=function(spread) { n=length(spread)

Hi, I am new in R and stumbled on a problem my (more experienced) friends can not help with with. Why isnt this code working? The function is working, also with the loop and the graph appears, only when I build another loop around it (for different values of p) , R stays in a loop? Can't it take more then 2 loops in one program? powerb<-function(x,sp2,a,b,b1,m) {

Hello, We are porting openssh-3.1p1 onto SX-6 running on SuperUX. We landed into problem when we started running sshd with the default encryption settings. As you would have already seen on this mailing list. Basically we are facing two problems (both client and servers run on SX):- 1) If the we use the default encryption algorithm aes128-cbc then we get a Bad Packet length problem on

Sorry for post a lot of things, for the first part of code, I copied my C++ iter macro by mistake(and you can see an explicit type casting). Here is the macro definition from R_exts/Itermacros.h #define ITERATE_BY_REGION_PARTIAL(sx, px, idx, nb, etype, vtype, \ strt, nfull, expr) do { \ * const** etype *px = DATAPTR_OR_NULL(sx); *

Hi devel team, I'm working on C/C++ level ALTREP compatibility for a package. The package previously used pointers to access the data of a SEXP, so it would not work for some ALTREP objects which do not have a pointer. I plan to rewrite the code and use functions like get_elt, get_region, and get_subset to access the values of a vector, so I have a few questions for ALTREP: 1. Since an

I'm experiencing similar problems with a 3C996-T under 4.8-REL. In particular, connecting a 4.8-REL machine to a 5.1-REL machine leads to some interesting situations: I can do simple pings across the link, but ssh fails, and heavy pings crash the 4.8 machine. Similarly changing the interface configuration with ifconfig tends to crash the 4.8 machine (mtu, link0, up/down, etc). The

I can bootstrap from observed distribution using 'sample'. But now, the challenge is to bootstrap from a frequency distribution. I have already smoothed the distribution and the next step is to bootstrap from the frequency distribution. I did numerous searches and found nothing. Last, need to transform percentile to z-score. Appreciate if anyone can tell how. Grace [[alternative HTML