similar to: Ridge regression

Hello, I have posted this mail a few days ago but I did it wrong, I hope is right now: I have the following doubts related with lm.ridge, from MASS package. To show the problem using the Longley example, I have the following doubts: First: I think coefficients from lm(Employed~.,data=longley) should be equal coefficients from lm.ridge(Employed~.,data=longley, lambda=0) why it does not happen?

Dear all I'm familiarising myself with Ridge Regressions in R and the following is bugging me: How does one get p-values for the coefficients obtained from MASS::lm.ridge() output (for a given lambda)? Consider the example below (adapted from PRA [1]): > require(MASS) > data(longley) > gr <- lm.ridge(Employed ~ .,longley,lambda = seq(0,0.1,0.001)) > plot(gr) > select(gr)

Hi all, I have run a ridge regression as follows: reg=lm.ridge(final$l~final$lag1+final$lag2+final$g+final$u, lambda=seq(0,10,0.01)) Then I enter : select(reg) and it returns: modified HKB estimator is 19.3409 modified L-W estimator is 36.18617 smallest value of GCV at 10 I think it means that it is advisable to

I'm trying to make a set of contour plots of bivariate kernel density estimates, showing three such plots overlaid, similar to this plot http://euclid.psych.yorku.ca/SCS/Private/Test/ridge-boot2.pdf except that I would like to have the contours *filled* (using transparent colors). To make this reproducible, I've saved the results of KernSmooth::bkde2D() in the following file:

Dear r-devel list members, On a couple of occasions I've encountered the issue illustrated by the following examples: --------- snip ----------- > mod.1 <- lm(Employed ~ GNP.deflator + GNP + Unemployed + + Armed.Forces + Population + Year, data=longley) > mod.2 <- update(mod.1, . ~ . - Year + Year) > all.equal(mod.1, mod.2) [1] TRUE > > f <-

Hello dear R help group, I have the following setup to analyse: We have about 150 subjects, and for each subject we performed a pair of tests (under different conditions) 18 times. The 18 different conditions of the test are complementary, in such a way so that if we where to average over the tests (for each subject), we would get no correlation between the tests (between subjects). What we wish

[This question is hopefully straight-forward, but difficult to provide reproducible code.] I'm doing a multivariate bootstrap, using boot::boot(), where the output of the basic computation is a k x p matrix of coefficients, representing a tuning constant x variable, as shown in the $t0 component from my run, giving a 3 x 6 matrix > lboot$t0 GNP Unemployed Armed.Forces

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]]

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

For an application of ridge regression, I need to get the covariance matrices of the estimated regression coefficients in addition to the coefficients for all values of the ridge contstant, lambda. I've studied the code in MASS:::lm.ridge, but don't see how to do this because the code is vectorized using one svd calculation. The relevant lines from lm.ridge, using X, Y are:

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

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

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 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"),

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]]

Hello everyone, I wanted to know if it was possible to change the color of certain leaves in a hclust object in order to make my graph more readable. I know I can color certain groups but I would like to enter a vector telling the plot function which leaves to color in which color. Thanks in advance, Eleni [[alternative HTML version deleted]]

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