similar to: Binary kernel discrimination

Dear colleague, Just an e-mail to know if they are people working in the field of chemoinformatic that are using R in their work. If yes I was wondering if we couldn't exchange tips and tricks about the use of R in this area ? Best regards Fred Ooms [[alternative HTML version deleted]]

I have been working on fitting Cox model for prediction by using rms package. I want to measure model's calibartion and discrimination. Discrimination was measured by using validate() in rms, Dxy can be transferred to Harrell's c index. But in this way, I cannot get 95%CI of c index. How can I do this in R? And by the way, what value should be in c index to present the model's well?

Hi! I have a question concerning the rcdk package: I generated a test sdf-file with 3 molecules in it and tried to perform clustering by fingerprints and plot the results in a dendogramm. This is what I did: mols <- load.molecules ("molecules.sdf") fp.list <- lapply (mols, get.fingerprint, 'maccs') fp.dist <- fp.sim.matrix (fp.list, method='tanimoto')

I anticipate lacking of prior experience with dimensionality reduction problems. Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another different equilibrium conformation. They sampled at regular intervals 7 dihedral angles, 5 bending angles, and

I've got a sample set of variables x1,...xn and a factor f that classifies each sample to belong to either group 0 or 1. If I build a model with m1<-glm(f~. , family=binomial(link="logit"),data=frame); pv<-as.vector(predict(m1)) prob<-plogis(pv) does then "prob" predict the probability of a sample to belong to group 1? Is this equivalent to logistic

Hi there, I can't seem to wrap my head around the differences between discrimination and calibration. I think that I learn best by examples. Could someone provide me with detailed explanations using examples of when a model could do both well, both poorly, and one well and the other poorly? Thanks! [[alternative HTML version deleted]]

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Hello, I am using logistic discriminant analysis to check whether a known classification Yobs can be predicted by few continuous variables X. What I do is to predict class probabilities with multinom() in nnet(), obtaining a predicted classification Ypred and then compute the percentage P(obs) of objects classified the same in Yobs and Ypred. My problem now is to figure out whether P(obs) is

Greetings, I would like to use a data.frame with strings to feed the expression() in the title of a plot. The way I did this is: molecules <-data.frame(name=c("o3","no","no2"),expression=c("quote(O[3])","quote(NO)","quote(NO[2])")) for (mol in c(5,7,9)) { plot(x, y, type="b",

hello , Iam working on the rcdk package ,when i start with it using the load.molecules fuction this is the error message returned Error in if (!file.exists(f) && !grep("http://", f)) stop(paste(f, ": Does not exist", : missing value where TRUE/FALSE needed could someone help me with this,thanks in advance regards Hari [[alternative HTML version deleted]]

<http://themoonlight.blogcu.com/5929751/>Can living things be created from dead and nonliving things? ** *Dr Metin GUNGORMUS * * ------------------------------ * ** ** *Atoms and molecules are not alive, and organelles are also not alive, but a living cell is a collection of non-living atoms and molecules. ( **From atoms to living organisms *

Hi, I am a method developer in drug discovery. I have developed a similarity searching method for small (drug-like) molecules. I want to compare the performance of my method to the performance of other methods. Similarity searching methods are commonly assessed by their ability to (re)discover a set of molecules that is avtive versus a given target, given one randomly selected query molecule.

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I have a dual stack server with Dovecot 2.1.10 listening on v4 and v6 Dovecot has a Comodo SSL certificate issued via NameCheap that works as expected with IPv4 in 10-ssl.conf I have enabled these configuraction directives: ssl = yes ssl_cert = < /path/to/file.crt ssl_key = < /path/to/file.key ssl_parameters_regenerate = 202 hours If I

Hello R Users, I am interested in using R to generate quantitative structure-activity relationships (QSARs) for small molecules given a set of molecular descriptors (the X's) and biological data (Y's) (usually tab-delimited data files). Has anyone done this using R ? Would you be willing to share your R scripts (or ideas) for doing this with me ? I am particularly interested in

> BTW, can someone explain to a libart major like me (;-)) where echo > comes on in a telephone conversation? I seem to recall it's due to the > length of the line between the CO and the local party, but I'm not > sure. I'll try. Echo occurs when part of the signal traveling in one direction on the phone line, is reflected back in the opposite direction. It's similar

Hello, I am looking for any packages, tutorials, documents,... about the use of R for the analysis of HTS data. Thanks for your help Fred [[alternative HTML version deleted]]

-----BEGIN PGP SIGNED MESSAGE----- ============================================================================= FreeBSD-SA-00:52 Security Advisory FreeBSD, Inc. Topic: TCP uses weak initial sequence numbers Category: core Module: kernel Announced: 2000-10-06

Dear All, I am looking at discriminating among several individuals based on a few variable sets (I think some variables do not make sense unless they are entered together, so I "force" them into the models together, hence datasets). I have done so with linear discriminant analysis (LDA) using "MASS::lda", with acceptable results. However, one of my collaborators

Dear time-series specialist: I've got some time series representing measurements from a physical process, like atomic decay data. These time series look almost random, but should hopefully be distinguishable as they were taken under different conditions. I am looking for statistical approaches that are sensitive enough to discriminate between such series of measurements. Preferably, there

I'm evaluating * to replace the crap set of peered "smart" phones we have now in our small office, but I haven't been able to find out about this anywhere yet: I need to know if * can discriminate _incoming_ FAX calls on a voice line and route them to a specific extension? We have a little standalone box to do this now, but only for one line, and if that line is busy---we