similar to: coloring leaves in clustering

Hi all, I am trying to draw a Kaplan-Meier curve and I found online that Kaplan - Meier estimates are computed with a function called km in the event package. Is there an update for that because when I choose to download packages in R,. there is no package called event, even though I have selected all the repositories. Thanks in advance, Eleni [[alternative HTML version deleted]]

Hello list, I am trying to apply the paired t.test between diseased and not diseased patients to identify genes that are more expressed in the one situation under the other. In order to retrieve the genes that are more expressed in the positive disease state I do: p.values<-c() for(i in 1:length(Significant[,1])){ p.values[i]<-try(t.test(positive[i,],negative[i,],alternative

Hi list! I have recently tried to take my office work home, meaning that I tried to transfer my "... .RData" workspace from my PC on my laptop. The office PC runs on Windows XP and my laptop runs on Windows Vista. I have saved the workspace at the office PC and kept it in a usb drive. When I tried to open it on my laptop I got an error: "Fatal Error: Unable to restore saved data in

Hi all! I am new to R and I would like to ask you the following question:How can I substitute the NA values with 0 in a data frame? I cannot find a command to check if a value is NA... Thank you very much! Eleni

Hi all, I am trying to install the package "GEOquery" in unix. I have downloaded the standard version of R and this package is not contained in the default. I know that I can select repositories under windows but I don't know how to do it in unix. Does anyone have any idea on this? Thank you in advance, Eleni [[alternative HTML version deleted]]

Hello R users, I am trying to run a cox model for the prediction of relapse of 80 cancer tumors, taking into account the expression of 17000 genes. The data are large and I retrieve an error: "Cannot allocate vector of 2.4 Mb". I increase the memory.limit to 4000 (which is the largest supported by my computer) but I still retrieve the error because of other big variables that I have in

Hello all, I have the following problem. I want to insert blank rows in an data frame so as to make it comparable with another data frame with more rows. How can I insert these rows? If this is not solvable, then, alternatively, is it easy to delete rows from a data frame? Thanks for helping, Eleni [[alternative HTML version deleted]]

Hello R community, I am processing raw Affymetrix CEL files and I am using the Michigan custom CDF library hgu133plus2hsentrezgprobe. I have been looking for documentation on the function that it contains...I am specifically interested in converting probe names to gene symbols. Does anybody know where I can find it? Thank a lot! Eleni [[alternative HTML version deleted]]

Dear list, I am trying to perform a significance analysis of a microarray experiment with survival data using the {samr} package. I have a matrix containing my data which has 17816 rows corresponding to genes, and 286 columns corresponding to samples. The name of this matrix is data.matrix2. Some of the first values of this matrix are: data.matrix2[1:3,1:5] GSM36777 GSM36778 GSM36779

I am trying to learn how to format Ascii data files for scan or read into R. Precisely for a quickie project, I found some code (at end of this email) to do exactly what I need: To cluster and graph a dendrogram from package (stats). I am stuck on how to format a text file to run the script. I looked at the dataset USArrests (which would be replaced by my data and labels) using UltraEdit. That

Dear list, I am having a set of human oligo ids (H200006022 H200002025 H300004703 H200000442 H200005719 H300018350) which I want to map to Ensembl or RefSeq. I am sure R has a function to do that. I downloaded the {oligo} package and tried to use the probeNames function. Although the factor of ologo ids is an object (as the argument to probeNames should be) I retrieve the following error:

Hello all! I am performingsome clustering analysis on microarray data using agnes{cluster} and I have created my own dissimilarity matrix according to a distance measure different from "euclidean" or "manhattan" etc. My question is, if I choose for example method="complete", how are the distances between the elements calculated? Are they taken form the dissimilarity

Dear list, I have a couple of questions concerning ridge regression. I am using the lm.ridge(...) function in order to fit a model to my microarray data. Thus *model=lm.ridge(...)* I retrieve some coefficients and some scales for each gene. First of all, I would like to ask: the real coefficients of the model are not included in the first argument of the output but in the result of coef(model),

Hello list! I have a proble trying to perform a SAM analysis using the function samr from the samr package. I have put the option *center.arrays=TRUE *in order to scale all the experiments to median=0. I would like to retrieved the scaled data but it seems that samr does not return it...Does anyone have any idea on this? Thanks a lot!!! E. [[alternative HTML version deleted]]

Dear list, I have been searching for a week to fit a simple linear model to my data. I have looked into the previous posts but I haven't found anything relevant to my problem. I guess it is something simple...I just cannot see it. I have the following data frame, named "data", which is a subset of a microarray experiment. The columns are the samples and the rows are the probes. I

Hello list, I am trying to perform ROC analysis and count the AUC in order to validate my results. I use package ROCR. I would like to count the AUC not under the cutoff found by "performance" but to use another cutoff that I calculate. How could I change the following command in order to get what I want? perform=performance(pred,measure="auc",x.measure="cutoff"),

Dear R users, I am trying to apply SVM regression for a set of microarray data. I am using the function svm() under the package {e1071}. Can anyone tell me what the *residuals *value represents? I have some observed values *y_obs* for the parameter that I want to estimate and I would expect that *svm$residuals = y_obs - svm$fitted. *However, this does not happen...Does anyone have any idea on

Dear list, I have some difficulty in manipulating list elements. More specifically, I am performing svm regression and have a list of lists, called pred.svm. The elements of the second list are 3D arrays. Thus I have pred.svm[[i]][[j]], with 1<=i<=5 and 1<=j<=20. I want to take the sum of the elements a specific array dimension across all j, for one i. Mathematically speaking, I want

Hello, I am a new R user and have a question regarding dendrogram coloring. I would like to color each leaf in the dendrogram (dhc) according to a specific criterion. For me this criterion is the gene name. For this, I created a data.frame with 2 variables: The gene name and the corresponding color. Using the following function, adapted from "dendrapply {stats}", I still have the same

Hi I have a distance matrix which is computed by user defined method. I would like to plot the dendrogram. I would like to use different color and want the leaves laying down bottom. The script like this. I am not familiar with R. I followed the example shown in http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html dist.obj <- as.dist(matrix.distance) hc.obj <-