similar to: Extract Clusters from Biclust Object

Hi, I was trying to draw a heatmap of the bicluster results. With the code given in the biclust package I can only get the heatmap for one cluster at a time (drawHeatmap function). Is there any way that I can get the heatmap for all the clusters at the same time? The code that I am using (biclust documentation) is: #Random 100x50 matrix with a single, up-regulated 10x10 bicluster

Hi, I wanted to compare the quality of biclusters obtained from the various biclustering algorithms. Is there a function/metric in biclust (or some other package) that will enable me to do this? thanks! [[alternative HTML version deleted]]

Hi R users,   I am trying to do two-way clustering (using information of both observation and variables). Is there any package available in R. Another querry, if somebody can provide related information (website) regarding this statistics, it will be great. Thanks in advance.   Regards,   Ram Kumar Basnet, Wageningen University. [[alternative HTML version deleted]]

I have a dataframe in which I have values 0-255, I wish to transpose them such that: if value > 127.5 value = 1 if value < 127.5 value = -1 I did something similar using the "binarize" function of the biclust package, this transforms my dataframe to 0 and 1 values, but I wish to use -1 and 1 and looking for a way in R to do this. Brian

I have a dataframe that has a header like so: class value1 value2 value3 class is a factor the actual values in the columns value1, value2 and value3 are 0-255, I wish to binarize these using biclust. I can do this like so: binarize(dataframe[,-1]) this will return a dataframe, but then I lose my first column class, so I thought I could combine it like so: dataframe <-

Hi there I have a list that looks like this object1 object1 78 object1 object2 45 object1 object3 34 object1 object4 45 object2 object2 89 object2 object3 32 object2 object4 13 but i want to create a matrix like this in order to use the dist function of R object1 object2 object3 object4 object1 78 45 34 45 object2 45

Dear all, I've started working with R (vs 1041) a few weeks ago, and now I'm having problems with the amount of memory. I'm working on the windows-me, my computer has 128 Mb of memory. I'm using the R under the emacs (ESS-5.1.20) and it is started by the command: Rterm --min-vsize=10M --max-vsize=100M --min-nsize=500k --max-nsize=1M I've been had problems when executing a

Hi all, Suppose I want to set the values in a column to the log of the values of another column like so: object$LogDist <- log10(object$Distance) How do I loop through the objects if I have object1, object2, etc to perform this function? object1$LogDist <- log10(object1$Distance) object2$LogDist <- log10(object2$Distance) object3$LogDist <- log10(object3$Distance) I was trying to

Dear R users, I have two simple questions here, and hope someone can help me on this. Thanks in advance. 1. I have a list object lst=list(a1=matrix(rnorm(4),2,2), a2=matrix(rnorm(4),2,2),a3=matrix(rnorm(4),2,2)). Here I only use three elements for illustration, and in fact the length of lst, n, is unknown in advance. I want to define an object for each element of this lst, and the objects have

Hi R users,   I am doing multiscale bootstrapping for clustering through pvclust package. I have large data set (observations 182 and variables 5546). When i tried to make bootstrapping, then i got message as "Bootstrap (r = 0.5)............Error: cannot allocate vector of size 117.3 Mb". I am new R user and could not understand what is the problem and also don't know the easiet

Hi, I'm trying to figure out syntax R function rm() needs to remove all objects starting with same name. For example, if I have object1, object2, object3, i want to do an operation similar to UNIX rm object* Thanks. -- View this message in context: http://r.789695.n4.nabble.com/remove-multiple-objects-starting-with-same-name-tp4418694p4418694.html Sent from the R help mailing list

Dear all,   I was using older version of R (installed early). I install new version of R (R.2.9.0) but i could not find package "xlsReadWrite" to read Excel file. Is there any alternatives to read Excel file ? I hope it should be. I need help although it is minor querry. Thanks in advance.   Sincerely, Ram Kumar Basnet Wageningen University, The Netherlands   [[alternative HTML

Dear R users,   It may be very simple but it is being difficult for me. I have two vectors with some common string. And, i want to combine into a vector in such a way that it includes string from both vectors and make a unique.   For example:   x <- paste(rep("A",5),1:5,sep = ".") x [1] "A.1" "A.2" "A.3" "A.4" "A.5" y <-

Hi everybody,   I am doing principal component analysis (PCA) using "prcomp' function. When i did "Biplot", i did not found interesting result and it is based on Principal component (PC) 1 vs PC2. Now, i want to see"Biplot" in combination of either PC1 vs PC3 or PC2 vs PC 3. I did not get the ideas. Does any one have ideas ? I am optimistic on getting some idea.

Dear all, I am trying to make barplot from matrix with "beside=FALSE". I have 165 labels in my bar plot. When i plot the label horizontally below the barplot, then all labels are not appear in the plot due to lack of space. I used the following function: barplot(t(bar), main="Barplot based on LCMS", ylab="RF membership Probability",   

Dear R Users, I am a novice learner of R software. I am working with Genetic Matching - GenMatch(), but I am getting an Error message as follows:  Error in GenMatch(Tr = Tr, X = X.binarynp, BalanceMatrix = BalanceMatrix.binarynp,  :    GenMatch(): input includes NAs Could you please suggest me correcting the above problem? My GenMatch command is, > gen1 <- GenMatch(Tr = Tr, X =

Dear R users,   I am using RandomForest package. While using this package, i got "Error: cannot allocate vector of size 117.3 Mb" .........................message. I had this problem earlier too but could not manage. Is there any way to solve this problem or to increase vector size ? My data set is of 163 samples and 5546 variables. I tried through "? Memory" function to solve

Hi   I think this may be simple task but creating trouble to me. In my calculation, i have got large number of rows (5546) and column 182 but i am not able to see all the rows. May be somebody have idea how i can see all the rows ? I will be greatful if any body help me. Thanks in advance   Sincerely, Ram Kumar Basnet Graduate student Wageningen University Netherlands   [[alternative

I have very large data set. I want to make subset of data based on the matching. For example,   > x [1] "a" "b" "c" "f" > yy                                                                     "a" "-0.761988113636315" "-0.117672628171555" "-0.885641151614679" "b" "-1.13288279283289" 

Hi R users, I want to calculate the partial correlation (first or second order) and their corresponding significance test (p-value). I used > library(corpcor) and "cor2pcor" function to calculate partial correlation but could not calculate "p-value". If some one knows the R package or function to calculate corresponding "p-value", It will be great help. Thanks