search for: biocomputing

...le to make use of zlib on effectively all > platforms, since it 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...

...and uncompression (e.g., using zlib or the bzip2 libraries) 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

...o `gzprintf' follow collect2: ld returned 1 exit status make[3]: *** [RJaCGH.dll] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-RJaCGH] Error 2 *** Installation of RJaCGH failed *** -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz

...ockets, etc, directly from R. However, Simon's comment about better ways of R-to-R communication made me wonder if this idea really makes sense. What is the catch? Have other people tried similar approaches? Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz

...m running one R script to plot many graphs it is in the for loop. its showing no error but its not plotting well I think i can solve this problem with a wait function. Please help me in this regards. If u need any clarification about programme. u can find the script below. best regards, Deepak.M.R Biocomputing Group University of Bologana. #!/usr/bin/R s<-c("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","...

Hola, ¿Alguien sabe cómo lidia la función aov con diseño no balanceado? ¿Utiliza el las funciones de suma de cuadrados type II ? Gracias!! [[alternative HTML version deleted]]

Dear all, I wonder which R algorithm could perform a mountain clustering in an spatial grid, in other words, having the coordinates of a map (x,y ... or even more) and then the altitude/height at each point I would like to localise the peaks of that topological surface. Which R algorithm can perform this? I see it as a clustering problem where the peak should be at the center of each cluster.

I have successfully installed ADaCGH package, and trying the example in SegmentPlotWrite did produce alot of pngs and html. I tried again the same example this morning (after a long night of installation), ADaCGH crashes at mpiInit() showing the error: Loading required package: Rmpi ELAN_EXCEPTION @ --: 6 (Initialisation error) elan_init: Can't get capability from environment Aborted I

...r method? I also have another question: How does lm() choose the point through which the output straight line goes in order to compute the values of its slope and intercept? I would be very grateful if anyone could help me. Domenico ********************************************* Domenico Cozzetto Biocomputing group Department of Biochemical Sciences "A. Rossi Fanelli" University of Rome "La Sapienza" P.le Aldo Moro, 5 - 00185 Rome Tel: +39 06 49690276 Fax: +39 06 4400062 URL: http://cassandra.bio.uniroma1.it/~cozzetto/

Dear R People: I am having some trouble with the snow package. It requires MPICH2 and Rmpi. Rmpi is fine. However, I downloaded the MPICH2 package, and installed. There is no mpicc, mpirun, etc. Does anyone have any suggestions, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto:

Hi All: Has anyone analyzed Illumina 550K data using DNAcopy package? I have around 2300 samples. According to Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single sample for Affymetrix 100K. I am afraid it will take too long to analyzed my data. Anybody has an idea? Thanks! Best, -- View this message in context:

...gnu system x86_64, linux-gnu status Patched major 2 minor 10.0 year 2009 month 11 day 05 svn rev 50317 language R version.string R version 2.10.0 Patched (2009-11-05 r50317) -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019

Hello, I was using snow to parallel-process some code in R-2.10 (32-bit windows. ). The code is as follows: require(foreach) require(doSNOW) cl <- makeCluster(6, type='SOCK') registerDoSNOW(cl) bl2 <- foreach(i=icount(length(unqmrno))) %dopar% { (some code here) } stopCluster(cl) When I run the same code in Windows R-2.11 (either 32-bit or 64-bit), R hangs at

...ifferent). I guess this is some sort of strange interaction between Windows and the virtualization, and R probably has little to do in this. However, has anybody been able to run snow and/or snowfall with socket clusters in a similar setup? Best, R. -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972

...problem. The package should be fixed anyway. Many thanks for your valuable work. Christian Bolliger -- ============================================================================= Christian Bolliger IT Services | http://www.id.unizh.ch/ Central Systems / Biocomputing | http://www.bio.unizh.ch/ University of Zuerich | E-Mail: christian.bolliger at id.unizh.ch Winterthurerstr. 190 | Tel: +41 (0)1 63 56775 CH-8057 Zuerich; Switzerland | Fax: +41 (0)1 63 54505 My PGP-Keys: http://www.id.unizh.ch/publications/ueber/visitenk/chribo.html

...llation in each network class. Thanks, Gerhard Mueller -- +-------------------------------------+-----------------------------+ | Gerhard Mueller | Phone: +49-3641-65-6204 | | Institut fuer Molekulare | Fax: +49-3641-65-6210 | | Biotechnologie (IMB), Biocomputing | | | Beutenbergstrasse 11, PF 100 813 | Email: gmueller@imb-jena.de | | D-07708 JENA | | +-------------------------------------+-----------------------------+

...except for the return of values into R). Another would be to write to a file from C and then read that into R, but this looks very ugly. Are there any other reasonable alternatives, or should I just use .Call? Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz

Hello R-helpers, I am trying to search for string that includes the caret symbol, using the following code: grepl("latitude^2",temp) And R doesn't like that. It gives me: > temp<-c("latitude^2","latitude and latitude^2","longitude^2","longitude and longitude^2") > temp [1] "latitude^2" "latitude and

when i plot with the following command on console: $ R CMD BATCH cp_messung.R in the R-script i wrote x11() in the beginning, so it draws a nice plot on my screen. But sadly it disappeares after a second or two. How can i make it to wait until i press a key or something? thank you. -- kind regards, Jonas Stein <news at jonasstein.de>

Hola, creo tener un problema por que me suscribí a la lista hace varios días y nunca he recibido mensajes.... puede ser???? Como debería hacer para solucionarlo?? saludos Germán Lic. Germán García Ecología y Conservación de Aves Marinas Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - CONICET Funes 3250 (B7602AYJ) Mar del Plata,