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...py of the first ed. of that wonderful book is falling apart). I would appreciate suggestions about other comparable books which, if possible, have examples using R/S code (instead of SAS). Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) http://bioinfo.cnio.es/~rdiaz

...inary response from a logistic regression model) The output plot was fine but it did not include the confidence intervals Anyone knows how to do it? (xYplot did not work either) many thanks - juan -- Juan F. Poyatos Structural and Computational Biology Programme Spanish National Cancer Centre (CNIO) Melchor Fernandez Almagro, 3/E-28029 Madrid SPAIN Phone:+34 912 246 900/Fax: +34 912 246 980 http://bioinfo.cnio.es/~jpoyatos/ **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}

...=20 minor 0.0 =20 year 2004 =20 month 04 =20 day 30 =20 language R =20 =2D-=20 Ram=F3n D=EDaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol=F3gicas (CNIO) (Spanish National Cancer Center) Melchor Fern=E1ndez Almagro, 3 28029 Madrid (Spain) =46ax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz PGP KeyID: 0xE89B3462 (http://bioinfo.cnio.es/~rdiaz/0xE89B3462.asc)

...f the initial model). So nothing really new. But I haven't been able to find any comments in the literature about "simplification" of random forests. Any suggestions/comments? Best, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz

...ery same list without the NULL components (i.e., I do not want to unlist or otherwise loose the rest of the list structure). I can do that with a loop, but how could I do it without a loop? Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz

...to replace is not a multiple of&nbs p;replacement length) -- ******************************************** Raquel Martinez Garcia, Graduate Student Gastrointestinal Cancer Clinical Research Unit & Structural Biology and BioComputing Programme Spanish National Cancer Research Center (CNIO) Melchor Fernandez Almagro, 3. 28029 Madrid, Spain. Phone: +34 91 732 80 00 #3015 rmartinezg@cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:7}}

Hi all, I would like to do some QSAR analysis (quantitative structure activity relationship). I need to use some Partial Least Squares (PLS) regression, but I have not seen this option on the R-project. Is it possible to do this kind of regression on R? thank you in advance best regards, olivier [[alternate HTML version deleted]]

Ich habe in R eine Version von SIR gefunden und ausprobiert. Leider kann diese multivariate Responses nicht verarbeiten. Gibt es in R eine ausgefeilte Version von SIR?

...hat this might be the obvious, unproblematic way to go, but I understood that stratified resampling was OK only when that was sampling scheme that generated the data. What am I missing? Thanks, R. -- Ram??n D??az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol??gicas (CNIO) (Spanish National Cancer Center) Melchor Fern??ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz PGP KeyID: 0xE89B3462 (http://bioinfo.cnio.es/~rdiaz/0xE89B3462.asc)

...i686, linux-gnu status major 1 minor 6.2 year 2003 month 01 day 10 language R -- Ramón Díaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncológicas (CNIO) (Spanish National Cancer Center) Melchor Fernández Almagro, 3 28029 Madrid (Spain) http://bioinfo.cnio.es/~rdiaz

...ith the following error message: Error in grid.pack(frame = key.gf, row = 1, col = 1, grob = grid.rect(x =rep(0.5, : unused argument(s) (frame ...) Are there any solution? Thanks in advance H -- ......................................................... Hernan J. Dopazo Bioinformatica. CNIO c/ Melchor Fern?ndez Almagro 3 28029, Madrid, Espa?a Tfn: (34) 91 224 69 00 ext: 2428 Fax: (34) 91 224 69 23 http://bioinfo.cnio.es .........................................................

To avoid angry replies, let me first say that I know that the use of Type III sums of squares is controversial, and that some statisticians recommend instead that significance be judged using the non-marginal terms in the ANOVA. However, given that type III SS is also demanded by some… is there a function (equivalent to drop1 for lm) to obtain type III sums of squares for mixed models using the

To anyone who can help, I have two stupid questions, and one fairly intelligent question Stupid question (1): is there an R function to calculate a factorial of a number? That is...is there a function g(.) such that g(3) = 6, g(4) = 24, g(6) = 720, etc? Stupid question (2): how do you extract the estimated covariance matrix of the random effects in an lme object? Intelligent question

...come a contributed package, and FA is not supposed to be used directly by an end user. I am aware of scoping differences between the three approaches, but that is not my main concern now). Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) http://bioinfo.cnio.es/~rdiaz

...t has a public interface on Windows. > > > > > > > Thanks, > > > > R. > > > > -- > > Ramon Diaz-Uriarte > > Statistical Computing Team > > Structural Biology and Biocomputing Programme > > Spanish National Cancer Centre (CNIO) > > http://ligarto.org/rdiaz > > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road,...

How do I cite a package (not R itself - I know how to do that)? Any thoughts or links? Many thanks in advance? Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology/

...system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R ----- Ramón Díaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncológicas (CNIO) (Spanish National Cancer Center) Melchor Fernández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz

...ies) and then use readBin, etc, from R. But, if I can, I'd like to avoid our C code having to call zlib, etc, so as to make our package easily portable. Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz

Hi All, Sorry if this is a repost (a quick browse didn't give me the answer). I wonder if there are packages that can do the feature selection and classification at the same time. For instance, I am using SVM to classify my samples, but it's easy to get overfitted if using all of the features. Thus, it is necessary to select "good" features to build an optimum hyperplane (?).

Hi, I looked for the nls() function and couldn't find it. In the refman.pdf it's mentioned as part of the nls package which I cannot find and I also read something about the MASS package, also impossible to find for me. Kris -- ------------------------------------------------------------------------ http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=krisn