search for: biol

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in c("BCR/ABL", "ALL1/AF4") : unused argume...

I stumbled across this link and was wondering if this has any relation to the R project. http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/R/index.html -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://w...

...i evrybody, in a matrix consisting of 49 columns, I would like to plot all columns against the first in 48 different graphs. Can you help me? Thank you in advance Sebastian -- *************************************************************************************************************** Dipl. Biol. Sebastian Krug PhD - student IFM - GEOMAR Leibniz Institute of Marine Sciences Research Division 2 - Marine Biogeochemistry D?sternbrooker Weg 20 D - 24105 Kiel Germany Tel.: +49 431 600-4282 Fax.: +49 431 600-4446 email: skrug at ifm-geomar.de

Hi, concerning my earlier mail, maybe someone has noted from the variable names that I try to analyse mircoarrary experiments. Does anybody know of a R-implementation of the two-step mixed-model normalization procedure proposed by Wolfinger et al. (2001) J. Comput. Biol. 8:625-637? That would be great, best, joerg

I have some data files in which some fields have multiple values. For example first last sex major John Smith M ANTH Jane Doe F HIST,BIOL What's the best R-like way to handle these data (Jane's major in my example), so that I can do things like summarize the other fields by them (e.g., sex by major)? Right now I'm processing the files (in excel since they're spreadsheets) by duplicating lines with two values in the...

...3 a b c 4 b c 4 b c NA 5 c 5 c NA NA What is my mistake? Thank you Sebastian -- *************************************************************************************************************** Dipl. Biol. Sebastian Krug PhD - student IFM - GEOMAR Leibniz Institute of Marine Sciences Research Division 2 - Marine Biogeochemistry D?sternbrooker Weg 20 D - 24105 Kiel Germany Tel.: +49 431 600-4282 Fax.: +49 431 600-4446 email: skrug at ifm-geomar.de

...ariable contained in the Y matrix. It is not a true MANCOVA that do a significance test (most often a Wald test) for the overall two sets comparison. Such a test is available in SPSS and SAS, but I really want to stay in R! Someone have any idea? Thanks in advance for your help!   Rémi Lesmerises, biol. M.Sc., Candidat Ph.D. en Biologie Université du Québec à Rimouski remilesmerises@yahoo.ca [[alternative HTML version deleted]]

Hello, I am trying to make a heatmap in R and am having some trouble. I am very new to the world of R, but have been told that what I am trying to do should be possible. I want to make a heat map that looks like a gene expression heatmap (see http://en.wikipedia.org/wiki/Heat_map). I have 43 samples and 900 genes (yes I know this will be a huge map). I also have copy numbers associated with

...mat<-as.matrix(read.table("vmat")) Xm<-vmat[1:22,1:20] hemd<-read.table("threehem",header=T) Ym<-as.matrix(hemd[,2]) gvdw.pls<-plsr(Ym ~ Xm,6,method="kernelpls") rsltv<-predict(gvdw.pls,comps=6) plot(Ym,rsltv,type="n",xlab="Actividad + Biol??gica",xlim=c(4.6,6),ylim=c(4.8,6),ylab=" Act. + Biol.(Pred.)",main="QSAR Ligaci??n de Derivados de la Artemisina con + Hemina",sub="Descriptores de Coeficientes VdW") text(Ym,rsltv,labels=threehem$cpd) text(Ym,rsltv,labels=hemd$type,adj=c(0,-1)) --------------...

I am trying to compute the periodicity of a time series. I would like to know which function in R does it. Also, how do I plot a Enright / Chi-square periodogram using R ? ( Enright, J.T., 1965, Journal of Theoret. Biol. 8,426-468) Greatly appreciate your help. Thanks in advance, Sukhaswami Malladi *************************************************************************** The contents of this communication are intended only for th...{{dropped}}

....327 0.081 0.162 0.143 #treatment2-treatment1 -0.074 -0.227 0.327 0.821 0.821 0.821 ___ drs. René Eschen CABI Bioscience Switzerland Centre 1 Rue des Grillons CH-2800 Delémont Switzerland +41 32 421 48 87 (Direct) +41 32 421 48 70 (Secretary) +41 32 421 48 71 (Fax) <http://www.unifr.ch/biol/ecology/muellerschaerer/group/eschen/eschen.html>http://www.unifr.ch/biol/ecology/muellerschaerer/group/eschen/eschen.html [[alternative HTML version deleted]]

...on? I'm not firm in statistics and didn't found anything about weighted averaging in combination with PLS in the help archives. Or is it possible to develop a workaround with the pls-package? thanks for help in advance Andreas Plank -- _____________________________________________ Dipl. Biol. Andreas Plank FU Berlin Institute of Geological Science Department Palaeontology Malteserstr. 74-100, House D 12249 Berlin Germany phone.: +49(0)30-83870-271 fax.: +49(0)30-83870-745 http://userpage.fu-berlin.de/~jevers/plank_a.htm

...stalled properly (does not get an installed version entry and is not loadable). If installed system wide it works. The package I installed is xgobi. MAC OS X 10.4.1 Volker - - - - - - - - - - - - - ------ ---- ---- --- -- - - - - - - - - - - - - - - - Dipl.-Biol. Volker Runkel Lehrstuhl f. Zoologie II www.biologie.uni- erlangen.de/zoo2 Staudtstr. 5 Telefon: 09131-85 28788 91058 Erlangen vrunkel@biologie.uni- erlangen.de - - - - - - - - - - - - - ----...

...t ci.tuwien.ac.at. Are these email adresses still valid? Best, Philippe Grosjean ...........]<(({?<...............<?}))><............................... ) ) ) ) ) __ __ ( ( ( ( ( |__) | _ ) ) ) ) ) | hilippe |__)rosjean ( ( ( ( ( Marine Biol. Lab., ULB, Belgium ) ) ) ) ) __ ( ( ( ( ( |\ /| |__) ) ) ) ) ) | \/ |ariculture & |__)iostatistics ( ( ( ( ( ) ) ) ) ) e-mail: phgrosje at ulb.ac.be or phgrosjean at sciviews.org ( ( ( ( ( SciViews project coordinator (http://www.sciviews.org) ) ) ) ) )...

...variables of this kind which I plan to test seperately - the amount of zeroes ranges from 75 to 97%.. I searched the web and found several modelling approaches but have the feeling that they are overly complex for my very simple dataset. Thanks in advance for any help! Kay -- Kay Cichini, MSc Biol Grubenweg 22, 6071 Aldrans Tel.: 0650 9359101 E-Mail: kay.cichini@gmail.com Web: www.theBioBucket.blogspot.co.at<http://www.thebiobucket.blogspot.co.at/><http://www.theBioBucket.blogspot.co.at> -- [[alternative HTML version deleted]]

...9;s system requirements. How many MB RAM and what processor speed would you recommend for Win XP if I want to load QuantArray Excel output files of appr. 16 MB each? Thank you very much in advance, Derk Bemeleit ----------------------------------------------- A--------T T-------A Dipl.-Biol. Derk Bemeleit G-----C Lab: A 4.65 T-A Gene Center and Institute of Biochemistry A-----T University of Munich G--------C Feodor-Lynen-Str. 25 C--------G 81377 Munich A-----T Germany G-C Tel: +49 (0) 89 2180-76961 T-----A Fax: +49 (0) 89 2180-7699...

...o de Fomento Pesquero - IFOP >> >> Valparaíso - Chile >> >> +56-32-21514 <callto:+56-32-2151424>42 >> >> >> >> www.ifop.cl >> >> >> >> -- >> >> C*ertificación ISO 9001/2008*: Sistema de Datos >> >> Biológico-Pesqueros (Arica, >> >> Iquique, Coquimbo, Valparaíso, San Antonio, Talcahuano y Calbuco, >> >> pesquerías industriales y artesanales) >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> __________________...

...ommands BBtraj <- list() for (i in 1:(nrow(loc@data)-1)) { BBtraj[[i]] <- kernelbb(as.ltraj(loc@coords[i:(i+1),], date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]), typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5, grid = 1000) }   Rémi Lesmerises, biol. M.Sc., Candidat Ph.D. en Biologie Université du Québec à Rimouski remilesmerises@yahoo.ca [[alternative HTML version deleted]]

Help! I've done this before but can't remember how to do it, and can't find any reference to it in the docs I have access to now. I need to increase --vsize (I think), as I'm getting a message when I start my R session "vector heap too small to load data". How does one exactly do this, and what is the default setting? I don't know how much to increase it by. I know

...-0.876494 -0.481413 0.6127  0.002 **  CON_frs  0.904278  0.426944 0.4846  0.013 *   PRP_frs -0.997634  0.068755 0.9433  0.001 *** RUI_frs -0.648512 -0.761204 0.6243  0.004 **  --- Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1  P values based on 999 permutations.   Rémi Lesmerises, biol. M.Sc., Candidat Ph.D. en Biologie Université du Québec à Rimouski remilesmerises@yahoo.ca [[alternative HTML version deleted]]