similar to: Manhattan Plot

Dear Colleagues, We are attempting to create trees using R with our Ruby on Rails application. However, we are running into a problem involving the creation of the graphic. We would like them to be in either jpg or png format so that users can save, but due to a lack of control over our sever we are unable to start X11 server. Is there a way to create these images without using X11 server?

Hello everybody: I have just started using R, specifically the clustering packages. Despite the vastness of the functionality of the system, I have found it very flexible and intuitive. It has been great fun to experiment with it. Nevertheless, I am under tight time constraints to complete a cluster analysis of some data and need to come up with a "quick" solution for the following

Dear Colleagues, We are attempting to create trees using R with our Ruby on Rails application. However, we are running into a problem involving the creation of the graphic. We would like them to be in either jpg or png format so that users can save, but due to a lack of control over our sever we are unable to start X11 server. Is there a way to create these images without using X11 server?

I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said > r <- glm(brain.cancer~epilepsy+other.cancer, c3, > family=binomial(link="logit"), intercept=FALSE) which produced

Using Debian Sarge, samba, CUPS, and an HP G85 mutifunction with HPOJ to use the G85 USB connection, I've been able to get raw printing to work, and Point 'n' Print driver download to work, but not at the same time. The driver download was a chore, because of HP's proprietary install program. Had to install the driver locally to get the needed files and copy them manually to the

Dear R users I am analysing data from a group of twins and their siblings. The measures that we are interested in are all correlated within families, with the correlations being stronger between twins than between non-twin siblings. The measures are all calculated from survey answers and by definition have limited ranges (e.g. -5 to +5), though within the range they are approximately normally

Greetings in Christ our Saviour. I am having an enormous amount of difficulties trying to do something that should be quite easy. Obviously, I am missing something. I have read everything I can find on this, and have tried everything I can think of and more... I am trying to mount a Win98 drive on my Redhat 7.0 box. The mounting is no problem. However, when I log into my user account and try

Hello, I will be very obliged if someone can help me with this statistical R problem: I am trying to do a Pearson correlation on my datasets X, Y with randomization test. My X and Y datasets are pairs. 1. I want to randomize (rearrange) only my X dataset per row ,while keeping the my Y dataset as it is. 2. Then Calculate the correlation for this pair, and compare it to your true

Dear R users, When I run the following code, R crashes: require(cclust) x <- matrix(c(0,0,0,1.5,1,-1), ncol=2, byrow=TRUE) cclust(x, centers=x[2:3,], dist="manhattan", method="kmeans") While this works: cclust(x, centers=x[2:3,], dist="euclidean", method="kmeans") I'm posting this here because I am not sure if it is a bug. I've been searching

Hi, Tenfei, I have two group of data composed of gene mutation and deletion on specific sites. Will it be possible for me to use the Manhattan Plot for comparison? Thank you for you attention! Li-Wu Guo, Ph.D. Sent from Windows Mail [[alternative HTML version deleted]]

Hello, I am trying to create a simple Manhattan plot for a small list of 200 SNPs spread out in the genome in different genes. I have tried different functions (using ggplot2 and a function created by Stephen Turner, mhtplot etc.)-none of them work smoothly. Does anyone have a simple way to create the plot (not for all 22 chromosomes)- with the x axis showing the genes name and not the

Hi I've successfully installed Duke Nukem Manhattan Project, but when I try to start it, it prompts for the CD, although the CD is in the drive and the drive is set up properly in Wine settings. It seems people have run the game successfully on wine, so perhaps someone's got a clue about this issue. Thanks for any help!

Greetings, I am reaching out to this mailing list with the following job opportunity. It is with a high-volume, heavy-traffic web property based in Manhattan. The job description is below. If interested please send an updated resume to nathan.madsen@algomod.com Regards, Nathan Madsen Algomod Technologies Corporation 116 John Street New York, NY 10038 Job # :

Dear List I am using R with mcgv package to model spatial variation in density estimates of dorcas gazelle in Sinai. I have 59 points of data and 4 explanatory variables(distance from mountain edge, camel presence, Latitude & Longitude). I want to test the model fir via bootstraping. I have used the jacknife bootstraping but it have the limitation of allowing only 58 trials. I tried to use the

I''ve heard that using LIKE is very slow, but I see it being used a lot in examples, blogs etc. Is it really that bad? Since Rails doesn''t directly support Fulltext search, this is the easiest way to get searching done, right? Or are there any other easier ways? I''m using acts_as_indexed right now, but it still doesn''t do what LIKE does.

Hi all, I have a matrix with 10000 rows and 10 columns. The last columns contains another identifiers but the values are not uniques so that I want to generate another matrix with rows with unique values in the last column. If I did tmp<-unique(my_mat$col10) this will give me 8560 unique entries so the ideal matrix will be 8560X10 columns now then. I tried sub_mat<-my_mat[tmp,] but

Dear R-users, A recent post (Feb 16) to R-help inquired about fitting a glmm with a negative binomial distribution. Professor Ripley responded that this was a difficult problem with the simpler Poisson model already being a difficult case: https://stat.ethz.ch/pipermail/r-help/2005-February/064708.html Since we are developing software for fitting general nonlinear random effects models we

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59

Full_Name: Yongchao Ge Version: 1.8 OS: Windows XP profesional Submission from: (NULL) (146.203.2.152) The R installation is fine on Windows XP, but when I started to open the R program, then it pops out this message: "R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience....." The error signature is: AppName: rgui.exe AppVer:

Is there some way to prevent finalizers running during a section of code? I have a package that includes R objects linked to database tables. To maintain the call-by-value semantics, tables are copied rather than modified, and the extra tables are removed by finalizers during garbage collection. However, if the garbage collection occurs in the middle of processing another SQL query (which is