search for: biomolecular

...eger(),endian="little",signed=FALSE) It works fine for n=10^8, but fails for n=10^9 (or even at n=6*10^8). My machine$sizeof.long is 8 bit. I am running R 2.13.1 on a x86_64-apple-darwin9.8.0/x86_64 (64-bit) architecture. Thanks for your help Florian -- AXA doctoral fellow Bundy lab - Biomolecular Medicine Imperial College London -- AXA doctoral fellow Bundy lab - Biomolecular Medicine Imperial College London [[alternative HTML version deleted]]

Hello, I am trying to place a legend in the title area of a plot. I can not seem to find a way to get legend() to do this. Nor can I use the title() function. Does anyone know a way to do this? I would greatly appreciate any advice. Thanks Josue Samayoa Center for Biomolecular Science & Engineering School of Engineering Division of Physical & Biological Sciences University of California Santa Cruz (831) 459-1019 [[alternative text/enriched version deleted]]

...le("data.txt",header=FALSE) for ( i in 1:nrow(file)) {  cat(file[i,1],":")  pvalue <- 2*(1-pnorm(abs(file[i,2])))  cat(pvalue,"\n") } can anyone help  me how to read the first column. regards Gaurav Kumar www.gauravkumar.org PhD Student, Chemistry and Biomolecular Sciences, Macquarie , Sydney, Australia. MS (Computational Biology), NCBS-TIFR, Bangalore, India. [[alternative HTML version deleted]]

...this could be happening and a fix for the problem, either from the Samba side or something that can be changed in the NT NETLOGON script? Thanks! Dan -- Dan K. Johnson Chief, Data and Information Services Risk Analysis and Information Management Branch Center for Coastal Environmental Health and Biomolecular Research NOAA - National Ocean Service Email: Dan.Johnson@noaa.gov Voice: (843) 762-8559 FAX: (843) 762-8700

Is there a way to determine the SVD of a complex matrix using R? (I'm using v1.0.1 and svd() won't do the trick). I know LAPACK has a function to do this. Thanks -- Ben Stapley Biomolecular Modelling Lab Imperial Cancer Research -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the...

...      beside=TRUE,           space=c(.1,1),           border="black",           col=c("blue","red") ) Please help me where i'm doing wrong or some known issue is there with boxplot. Thanks in advance. Gaurav Kumar www.gauravkumar.org PhD Student, Chemistry and Biomolecular Sciences, Macquarie , Sydney, Australia. MS (Computational Biology), NCBS-TIFR, Bangalore, India. [[alternative HTML version deleted]]

This is some interesting: > -8^(1/3) [1] -2 > x=(-8:8) > y=x^(1/3) > y [1] NaN NaN NaN NaN NaN NaN NaN NaN 0.000000 1.000000 [11] 1.259921 1.442250 1.587401 1.709976 1.817121 1.912931 2.000000 So, can anybody explain this?! (Why is x[1]^(1/3)=y[1]=NaN, but -8^(1/3)=-2?) Thx!!! [[alternative HTML version deleted]]

...this? It seems common to all windows systems I've tried. Is there a package I can install that will correct this? Best wishes, Harry -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Andrew Harrison Tel: 44 (0) 207 679 3890 Biomolecular Structure and Modelling Unit Fax: 44 (0) 207 679 7193 Biochemistry and Molecular Biology Dept. University College London Gower Street Email: harry at biochem.ucl.ac.uk London, WC1E 6BT, UK http://www.biochem.ucl.ac.uk/~harry ~~~~~~~~~~~~~~~~~~~...

Hi, I am trying to plot several columns in different graphs in columns and rows. The first column of my data file is the time, and the third is the 'elevation angle' with 19 different numbers. I would like to plot the rest of the columns with the x axis as time and the individual angles in different colours. Here is the code I am using right now. It plots the different columns with time,

...integer overflow in: n.x * n.y 2: NAs produced by integer overflow in: n.x * n.y 3: cannot compute correct p-values with ties in: ks.test(genomesv, scopv) Is there anything I can do about this? I'd realy like to know what the p-value is ;-) thanks a lot for help, Arne -- Arne Mueller Biomolecular Modelling Laboratory Cancer Research UK, London Research Institute 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone1 : +44-(0)20-72693405 | fax : +44-(0)20-75945789 phone2 : +44-(0)20-75945776 | mobil: +44-(0)7984601749 email : a.mueller at cancer.org.uk | http://www.bmm.icnet.uk...

...uses R. Sadly, I found out that the png and jpeg devices need an X-server :-( , so I cannot use these nice devices. Does any one have any experience using R for on-the-flycreation of graphics for web-pages pages? Any suggestions for workarounds? thanks very much for help, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-....

...#2    A   x2   5 #3    A   x3   2 #4    B   x1   3 #5    B   x2   7 #6    B   x3   3 #7    C   x1   4 #8    C   x2   10 #9    C   x3   5 Help needed as how i should provide list as a third argument to data.frame(). Thanks in advance. Gaurav Kumar www.gauravkumar.org PhD Student, Chemistry and Biomolecular Sciences, Macquarie , Sydney, Australia. MS (Computational Biology), NCBS-TIFR, Bangalore, India. [[alternative HTML version deleted]]

...e they are rather long (e.g. "H. sapiens", "D. melanogaster" ...). What is the easiest way to solve this problem, can I (somehow) re-scale the x-extension and x-shift the plot to get more space to the left of the visible area? thanks a lot for help, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-....

...ncol=200) M <- matrix(0,ncol=200,nrow=200) for (i in 1:nrow(Q)) M <- M + tcrossprod(Q[i,]) I would appreciate pointers to help me fill this lacuna in my R skills :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands

...y don't get it. Finally, I'd like to have the raw data-points together with a line representing the function used to fit the data in a plot? How can I plot function, e.g. sin(x) ? I hope I just need a primer on this to get going. thanks very much for any help, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-....

I am pretty new to R. So this may be an easy question for most of you. ? I would like to calculate the squared distances of a large set (let's say 20000) of vectors (let's say dimension of 5) to a fixed vector. ? Say I have a data frame MY_VECTORS with 20000 rows and 5 columns, and one 5x1 vector y. I would like to efficiently calculate the squared distances?between each of the 20000

...ystem. Best Regards, Davide -- Davide M. Marini, Ph.D. Research Fellow, Department of Cardiology Children's Hospital Boston | Harvard Medical School Enders 1306, 320 Longwood Avenue, Boston, MA 02115 Research Associate, Department of Materials Science Massachusetts Institute of Technology | Biomolecular Materials Group 77 Massachusetts Avenue, Room 16-244 Cambridge, MA 02139

...m directly with "xm info" I get: xen_major : 3 xen_minor : 1 xen_extra : .2-92.1.18.el5 Cheers, N. -- ============================================== Nuno Ricardo Santos Loureiro da Silva Ferreira NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Bloembergen gebouw Padualaan 8, 3584 CH Utrecht The Netherlands P: +31.(0)30.253 9932 F: +31.(0)30.253 2652 E: n.l.ferreira@uu.nl W: http://nmr.chem.uu.nl ============================================== _______________________________________________ Xen-users mailing...

Does anyone know of a R package that will determine the convex hull of a high-dimensional dataset (say 4-10 dimensions). I know chull works for 2D data. I'm neophyte to R and convex hulls so please keep it simple. Many thanks Ben -- Ben Stapley. Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD. Tel 0161 200 5818 Fax 0161 236 0409 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subsc...

...the same colour but a different finnling pattern. Is R able to do that? Anyway, it's not the end of the world if not, a workaround would be to export the plot in fig format and then using xfig to make the bar filling striped, dotted etc ... thanks for comments, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-...