Re: [R] comparing 2 long lists in R

Bogdan, I would look into bioconductor for packages handling this type choromosomal range data. cntools is one poped into my mind. Tao On Thursday, September 24, 2015 12:59 PM, Sarah Goslee wrote: merge() most likely, but: are these really lists in the R sense?

Re: [R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

open(fdf2) Am 26.06.2015 um 01:04 schrieb Shi, Tao: Hi all, I'm new to ff package through the using Bioconductor package crlmm.  Here is my problem: I've created a few R objects (e.g. an CNSet) using crlmm based on my data and save them in a .RData file.  crlmm heavily uses ff package

Re: [R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

, at 4:04 PM, Shi, Tao via R-help wrote: Hi all, I'm new to ff package through the using Bioconductor package crlmm.  Here is my problem: I've created a few R objects (e.g. an CNSet) using crlmm based on my data and save them in a .RData file.  crlmm heavily uses ff package to store

[R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

Hi all, I'm new to ff package through the using Bioconductor package crlmm. Here is my problem: I've created a few R objects (e.g. an CNSet) using crlmm based on my data and save them in a .RData file. crlmm heavily uses ff package to store results on a local folder. For certain reasons, I

[R] Error in title(...) : X11 font ....

Hi list, Could anybody help me to explain the following error message and fix it? Thank you very much! Tao sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8

[R] Rtools 3.3 is not compatible with R 3.2.0.?

hi list, Any updates on this issue? Thank you very much! Tao devtools::install_github(rstudio/packrat) WARNING: Rtools 3.3 found on the path at c:/Rtools is not compatible with R 3.2.0. Please download and install Rtools 3.1 from http://cran.r-project.org/bin/windows/Rtools/, remove the

Re: [R] interactive labeling/highlighting on multiple xy scatter plots

This is new to me.  Thanks for suggesting! Tao On Friday, August 1, 2014 3:05 AM, Michael Lawrence lawrence.mich...@gene.com wrote: You should check out the animint package. https://github.com/tdhock/animint On Mon, Jul 28, 2014 at 5:48 PM, Shi, Tao shida...@yahoo.com wrote: hi list

Re: [R] interactive labeling/highlighting on multiple xy scatter plots

/master/2014-01 On Thu, Jul 31, 2014 at 10:17 AM, Shi, Tao shida...@yahoo.com wrote: I looked at ggvis briefly before, but didn't notice its brushing capability.  Now you explained. Thanks, both! Tao On Wednesday, July 30, 2014 9:50 AM, Ramnath Vaidyanathan ramnath.vaidyanat

Re: [R] interactive labeling/highlighting on multiple xy scatter plots

, but the later is still an option for collaborators who do not have R installed. On Tue, Jul 29, 2014 at 2:13 PM, Shi, Tao shida...@yahoo.com wrote: Thank you very much, Greg and Ramnath, for the pointers!  I'll explore more. On Tuesday, July 29, 2014 8:10 AM, Ramnath Vaidyanathan

Re: [R] interactive labeling/highlighting on multiple xy scatter plots

require R to be installed. I don't know of any way to get what you want without installing at least one of ggobi or R (or some other program of similar complexity to install). On Mon, Jul 28, 2014 at 6:48 PM, Shi, Tao shida...@yahoo.com wrote: hi list, I'm comparing the changes of ~100 analytes

[R] interactive labeling/highlighting on multiple xy scatter plots

hi list, I'm comparing the changes of ~100 analytes in multiple treatment conditions.  I plotted them in several different xy scattter plots.  It would be nice if I mouse over one point on one scatter plot, the label of the analyte on that scatter plot AS WELL AS on all other scatter plots

Re: [R] tab auto-fill and arrow keys are not working in R on a linux cluster

--- Sent from my phone. Please excuse my brevity. On June 3, 2014 4:47:58 PM PDT, Shi, Tao shida...@yahoo.com wrote: Hi List, We have R 3.1.0 installed on the head node of our linux cluster, but the tab auto-complete and the arrow keys

[R] tab auto-fill and arrow keys are not working in R on a linux cluster

Hi List, We have R 3.1.0 installed on the head node of our linux cluster, but the tab auto-complete and the arrow keys are not working.  When I was trying to use the up/down arrow key to scroll through the old command history I got something like this.  Any ideas on what's going on here? Many

[R] code folding for both TeX sections and R code chunks in .rnw file

Hi list, Sorry, this is not a question directly for R, rather for R code editor.  I'm posting it here to capture wider audience. The problem I'm facing is that as sometimes my .rnw file gets bigger and bigger, navigating through it becomes an issue.  Scrolling back-n-forth or remembering the

[R] XML package installation -- an old question

Hi list, I have encountered the Cannot find xml2-config problem too during XML package installation on my 64-bit Redhat (v. 6.4) linux machine.  After looking through the old posts I checked all the necessary libraries and they all seem to be properly installed (see below).  I don't understand

Re: [R] XML package installation -- an old question

PATH. (You can also send _me_ the config.log file from the attempted installation.)   D. On 8/15/13 10:13 AM, Shi, Tao wrote: Hi list, I have encountered the Cannot find xml2-config problem too during XML package installation on my 64-bit Redhat (v. 6.4) linux machine.  After looking

[R] compare objects in two different workspaces

Hi list, Is there a easy way to compare objects in two different workspace files (i.e. .RData files) in R?  I can use some generic file compare softwares (e.g. BeyondCompare) to binary comparison, but when it says they're different you can't tell where the difference are from. Thanks! Tao

Re: [R] compare objects in two different workspaces

...@gene.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org r-help@r-project.org Sent: Thursday, February 7, 2013 1:30 PM Subject: Re: [R] compare objects in two different workspaces ... but you need to load them into different

Re: [R] compare objects in two different workspaces

Thanks, Bert!  Never used it, but reading it now. Tao - Original Message - From: Bert Gunter gunter.ber...@gene.com To: Shi, Tao shida...@yahoo.com Cc: R. Michael Weylandt michael.weyla...@gmail.com; r-help@r-project.org r-help@r-project.org Sent: Thursday, February 7, 2013 2

Re: [R] what's this character?

Thank you, Jim, Peter, and John, for your help!   Turns out it is a non-break space.  No idea how it got there (the file is from somebody else).  Thanks to Excel, I guess. Tao From: John j...@surewest.net To: r-help@r-project.org Cc: Shi, Tao shida

[R] what's this character?

Hi list, I've encounter this problem (see below).  I know it's particularly R-related and it's easy to get by but it still bothers me a lot.  It looks the last character of N.C. is a space to me, but it's clearly not.  Can someone tell me a way to figure out what character is in the last

[R] warning message

Hi list, Can somebody explain why there are these warning messages?  I just don't get it.  I'm using R 2.15.1 on WinXP. Thanks! Tao x [1] -2.143510 -1.157450 -1.315581  1.033562 -1.225440 -1.179909   ifelse(x0, log2(x), -log2(-x)) [1] -1.099975 -0.210950 -0.395700  0.047625 -0.293300

Re: [R] warning message

Never mind.  I got it.  Thanks! Tao - Original Message - From: Shi, Tao shida...@yahoo.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Monday, October 15, 2012 4:08 PM Subject: [R] warning message Hi list, Can somebody explain why there are these warning

Re: [R] warning message

Thank you, Simon and Kevin! Tao - Original Message - From: Simon Knapp sleepingw...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Monday, October 15, 2012 4:25 PM Subject: Re: [R] warning message T he second and third arguments

Re: [R] Sweave encoding option

this encoding option Still puzzled. Tao From: Yihui Xie x...@yihui.name To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, September 4, 2012 7:40 PM Subject: Re: [R] Sweave encoding option What happened might

[R] Sweave encoding option

Hi list, I was running Sweave on one of my .rnw file.  Everything was fine, until I came back from the vacation.  Nothing changed (at least to my knowledge), but now I have this problem: Sweave(myfile.rnw) Error: ‘COLO001final.rnw’ is not ASCII and does not declare an encoding After

Re: [R] .rda vs. .RData

Thank you, all! From: Barry Rowlingson b.rowling...@lancaster.ac.uk To: Jeff Newmiller jdnew...@dcn.davis.ca.us Cc: Shi, Tao shida...@yahoo.com; Ista Zahn istaz...@gmail.com; r-help@r-project.org r-help@r-project.org Sent: Tuesday, April 24, 2012 12:36 AM

[R] load only one object from a .RData file

Hi list, Is there a way to load one specific object from a .RData file which contains multiple data objects?  Thanks, ...Tao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] load only one object from a .RData file

Thank you, Michael and Henrik.  I'll try what you suggested. From: Henrik Bengtsson h...@biostat.ucsf.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, April 24, 2012 12:37 PM Subject: Re: [R] load only one

[R] .rda vs. .RData

Are they the same with .RData being the newer format?  Thanks, ...Tao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented,

Re: [R] barplot with both color and shading

Thank you both, Michael and Jim, for the answers! - Original Message - From: Michael Bibo michael_b...@health.qld.gov.au To: r-h...@stat.math.ethz.ch Cc: Sent: Wednesday, February 22, 2012 12:46 AM Subject: Re: [R] barplot with both color and shading Shi, Tao shidaxia

[R] barplot with both color and shading

Hi list, I want to draw a bar plot with color indicating one grouping and different shading on top of the color indicating another grouping.  How should I proceed? Thanks! ...Tao __ R-help@r-project.org mailing list

Re: [R] barplot with both color and shading

: barplot(1:10, angle=20, density=c(0,20), col=rep(0:1, each=5)) ...Tao - Original Message - From: R. Michael Weylandt michael.weyla...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, February 21, 2012 6:49 PM Subject: Re: [R] barplot

Re: [R] extract worksheet names from an Excel file

Thanks, Gabor!  That's really helpful! ...Tao - Original Message - From: Gabor Grothendieck ggrothendi...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Friday, June 24, 2011 5:02 AM Subject: Re: [R] extract worksheet names from

[R] extract worksheet names from an Excel file

Hi list, Is there a R function I can use to extract the worksheet names from an Excel file?  If no, any other automatic ways (not using R) to do this? thanks! ...Tao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] extract worksheet names from an Excel file

file   On 24/06/11 16:55, bill.venab...@csiro.au wrote: Package XLConnect appears to provide this kind of thing. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Shi, Tao Sent: Friday, 24 June 2011 2:42 PM To: r-help@r

[R] a bug in heatmap.plus?

Hi Allen and list, See the code below.  I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.  All gave the same results.  The problem is in the last line: when I tried to plot two different color bars, the one corresponding to cm.colors(10) is not correct (it starts

Re: [R] network package in R

Weiwei, I know this is not a Bioconductor-specific question, but you may also want to post it on BiC help list, as there may be more people there understand what you want to do. I'm also curious about the answers to your question. ...Tao - Original Message From: Weiwei Shi

Re: [R] changes in coxph in survival from older version?

Thank you very much, Frank and Terry, again, for all your answers! ...Tao - Original Message From: Terry Therneau thern...@mayo.edu To: Shi, Tao shida...@yahoo.com Cc: Frank Harrell f.harr...@vanderbilt.edu; r-help@r-project.org Sent: Fri, May 20, 2011 6:36:28 AM Subject: Re: [R

Re: [R] changes in coxph in survival from older version?

Thank you, Frank and Terry, for all your answers! I'll upgrade my survival package for sure! It seems to me that you two are pointing to two different issues: 1) Is stepwise model selection a good approach (for any data)? 2) Whether the data I have has enough information that even worth to

Re: [R] changes in coxph in survival from older version?

didn't even converge? Thanks! ...Tao - Original Message From: Terry Therneau thern...@mayo.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Thu, May 12, 2011 6:42:09 AM Subject: Re: changes in coxph in survival from older version? On Wed, 2011-05-11 at 16:11

Re: [R] changes in coxph in survival from older version?

Subject: Re: [R] changes in coxph in survival from older version? Please don't be serious about doing variable selection with this dataset. Frank Shi, Tao wrote: Hi Terry, Really appreciate your help! Sorry for my late reply. I did realize that there are way more predictors

Re: [R] R versions for Red Hat Linux

I second Marc on this. I just installed R2.12.2 on my linux box running RHEL. Now I also see R2.13.0 available by typing yum info R. ...Tao - Original Message From: Marc Schwartz marc_schwa...@me.com To: Marta Avalos marta.ava...@isped.u-bordeaux2.fr Cc: r-help@r-project.org

[R] changes in coxph in survival from older version?

Hi all, I found that the two different versions of survival packages, namely 2.36-5 vs. 2.36-8 or later, give different results for coxph function. Please see below and the data is attached. The second one was done on Linux, but Windows gave the same results. Could you please let me know

Re: [R] a bug in write.csv?

As pointed out by Ista, please read the help file. write.csv and write.csv2 provide convenience wrappers for writing CSV files. They set sep, dec and qmethod, and col.names to NA if row.names = TRUE and TRUE otherwise. From: John Kane jrkrid...@yahoo.ca

[R] read password-protected files

Hi list, I have a bunch of .csv files that are password-protected. I wonder if there is a way to read them in in R without manually removing the password protection for each file? Thank you very much! ...Tao [[alternative HTML version deleted]]

Re: [R] How to update R?

This question has been asked by many people already. The easiest way is: 1) install the new version 2) copy all or the libraries that you installed later from the library folder of older version to the new version 3) uninstall the old version 4) do a library update in the new version Done!

Re: [R] How to update R?

Forgot to mention that my way of updating is for Windows only. ...Tao From: Joshua Wiley jwiley.ps...@gmail.com To: Li, Yunfei yunfei...@wsu.edu Cc: r-help@r-project.org Sent: Thu, March 31, 2011 11:05:29 AM Subject: Re: [R] How to update R? Hi Yunfei, It

Re: [R] read password-protected files

this? Thanks! ...Tao From: Prof Brian Ripley rip...@stats.ox.ac.uk Cc: r-help@r-project.org Sent: Thu, March 31, 2011 11:15:35 AM Subject: Re: [R] read password-protected files On Thu, 31 Mar 2011, Shi, Tao wrote: Hi list, I have a bunch of .csv files

Re: [R] read password-protected files

Thanks, Josh. I use xlsReadWrite routinely. It would be nice if it has a password option. ...Tao - Original Message From: Joshua Wiley jwiley.ps...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Thu, March 31, 2011 11:50:27 AM Subject: Re: [R] read

Re: [R] read password-protected files

Thanks, Henrique! I'll try that. ...Tao - Original Message From: Henrique Dallazuanna www...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: Prof Brian Ripley rip...@stats.ox.ac.uk; r-help@r-project.org Sent: Thu, March 31, 2011 12:00:45 PM Subject: Re: [R] read password-protected

[R] confusion matrix

Hi list, Is there already a function somewhere to output the confusion matrix from two input vectors? table always automatically delete rows or columns with all 0's. For example, I would like the columns for 10 and 30 added back. Thanks! ...Tao 20 40 50 60 70 80 90 100 10 0 0

Re: [R] confusion matrix

Thanks, Richard, for your speedy reply! From: Richard M. Heiberger r...@temple.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Tue, March 8, 2011 12:28:05 PM Subject: Re: [R] confusion matrix You need to make your variables into factors and specify the levels. x - c

Re: [R] which functions are being debugged?

Hi Henrique, Thanks for the reply! I posted the question in a hurry yesterday. After a bit research today, I found that back in 2009, Andrew actually asked the same question and there was a good discussion about it:

[R] which functions are being debugged?

Hi list, Is there a function that can let me know which functions are being debugged? I know I'm probably not doing a very good job of keeping track of things, but it does get messier when you dig into different layers of a function. I know there is isdebugged, but it only works on one

Re: [R] UniCox in R

Hi Samuel, The help file explains which is which: A list with components devcvm Average drop in CV deviance for each lambda value ncallcvm=ncallcvm Average number of features with non-zero wts in the CV, for each lambda value se.devcvm Standard error of average drop in CV deviance for each

[R] given a sensitivity calculate specificity based on a ROC curve

Hi list, I know this is not hard to implement based on the returned objects from ROC, ROCR or a couple of other roc-related packages. I'm just wondering if there is already such a function exist. Thanks! ...Tao __ R-help@r-project.org mailing list

[R] question on uniCox

Hi list, I’m testing out uniCox R package (version 1.0, on R2.12.0, WinXP). When I ran uniCox on my data, there are always some NA’s in the beta matrix, which in turn causes problems in uniCoxCV call. I don’t see anything wrong with the corresponding data (e.g. no NAs) and if I fit a

Re: [R] calculating martingale residual on new data using predict.coxph

Thank you, Terry! - Original Message From: Terry Therneau thern...@mayo.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com Sent: Mon, November 22, 2010 6:11:15 AM Subject: Re: calculating martingale residual on new

Re: [R] calculating martingale residual on new data using

Thank you for the advice, Frank! ...Tao - Original Message From: Frank Harrell f.harr...@vanderbilt.edu To: r-help@r-project.org Sent: Sun, November 21, 2010 5:49:36 AM Subject: Re: [R] calculating martingale residual on new data using The tendency is to use residual-like

Re: [R] calculating martingale residual on new data using predict.coxph

Thank you, David! You've been always helpful! ...Tao - Original Message From: David Winsemius dwinsem...@comcast.net To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com Sent: Sun, November 21, 2010 5:50:31 AM Subject: Re

Re: [R] calculating martingale residual on new data using predict.coxph

...@comcast.net To: David Winsemius dwinsem...@comcast.net Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com Sent: Fri, November 19, 2010 10:53:26 AM Subject: Re: [R] calculating martingale residual on new data using predict.coxph On Nov

[R] calculating martingale residual on new data using predict.coxph

Hi list, I was trying to use predict.coxph to calculate martingale residuals on a test data, however, as pointed out before http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type=expected) is not implemented yet. Dieter suggested to use 'cph' and

Re: [R] calculating martingale residual on new data using predict.coxph

Hi David, Thank you for the quick reply! resid(fit) only gives the residuals on the training data not on test data. ...Tao - Original Message From: David Winsemius dwinsem...@comcast.net To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org; dieter.me...@menne-biomed.de

Re: [R] date calculation

Computing Facility Department of Statistics UC Berkeley ymailto=mailto:spec...@stat.berkeley.edu; href=mailto:spec...@stat.berkeley.edu;spec...@stat.berkeley.edu On Fri, 29 Oct 2010, Shi, Tao wrote: Hi list, Could

Re: [R] date calculation

- Original Message - From:Ben Bolker bbol...@gmail.com To:r-h...@stat.math.ethz.ch Cc: Sent:Friday, October 29, 2010 7:54:53 PM Subject:Re: [R] date calculation Shi, Tao shidaxia at href=http://yahoo.com;yahoo.com writes: Could someone explain to me why the following result

Re: [R] date calculation

Bolker bbol...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Sent: Saturday, October 30, 2010 7:22:04 AM Subject: Re: [R] date calculation On 10-10-30 02:02 AM, Shi, Tao wrote: Hi Ben, That must be the case! In fact if I do: difftime(strptime

Re: [R] date calculation

I think this demonstrate on of the differences between Class 'Date' and 'POSIXlt'. Thanks, Marc! ...Tao From: Marc Schwartz marc_schwa...@me.com To: Ben Bolker bbol...@gmail.com Cc: Shi, Tao shida...@yahoo.com; r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Sent: Saturday, October 30

[R] date calculation

Hi list, Could someone explain to me why the following result is not a integer? difftime(strptime(24NOV2004, format=%d%b%Y), strptime(13MAY2004, format=%d%b%Y), units=days) Time difference of 195.0417 days I'm using R2.12.0 on WinXP. Thanks! ...Tao

Re: [R] pairs with same xlim and ylim scale

after adding xlim and ylim. According to the error message, the two added parameters were not used in lower.panel, or the customized function f.xy. On 2010-9-1 2:26, Shi, Tao wrote: Hi list, I have a function which basically is a wrapper of pairs with some useful panel functions. However, I'm

[R] pairs with same xlim and ylim scale

Hi list, I have a function which basically is a wrapper of pairs with some useful panel functions. However, I'm having trouble to pass the xlim and ylim into the function so the x and y axes are in the same scale and 45 degree lines are exactly diagonal. I've looked at some old posts, they

Re: [R] R eat my data

Changbin, It looks you're trying to read in a gene annotation file and usually it has many strange characters, e.g. #, , (as other people also suggest). I encounter this all the time. So try to be very thorough about your search (the first place I'll look for is the line where R stop

Re: [R] doubt about samr siggenes.table$genes.up

Leo, This question is more suited for the BioC help list. Please post your question over there. Also, offer more info about how you arrived this siggenes.table, what version of R and siggenes package you're using would be helpful. Please read the posting guide! ...Tao - Original

Re: [R] Fast Matrix Computation

One way to do it: apply(B, 1, function(x) t(apply(A, 1, function(y) abs(y-x) )) ) - Original Message From: David Neu da...@davidneu.com To: r-help@r-project.org Sent: Sat, May 22, 2010 10:35:32 AM Subject: [R] Fast Matrix Computation Hi, I have two (large) matrices A and B

Re: [R] Concatenation

Well, it seems a simple c will do. e.g. df - matrix(rnorm(100), ncol=4) c(t(df[1:10,])) # concatenate rows c(df) # concatenate columns From: santana sarma aimanusa...@gmail.com To: Shi, Tao shida...@yahoo.com; r-help@r-project.org Sent: Thu, May 20, 2010 11:45:25 PM Subject: Re

Re: [R] p-values 2.2e-16 not reported

Will, I'm wondering if you have any insights after looking at the cor.test source code. It seems to be fine to me, as the p value is either calculated by your first method or a .C code. ...Tao - Original Message From: Will Eagle will.ea...@gmx.net To: r-help@r-project.org

Re: [R] About the breakpoint when making heatmap with lots of variables

The breakpoint you mentioned is irrelevant here. Clustering 15672 genes (I assume this is a microarray data) requires lots of memory. I suggest you either filter your gene list down to thousands or just plot the column dendrogram without showing the heatmap. plot(hclust(dist(x))) ...Tao

Re: [R] colored venn diagram

Thank you for the suggestions, Peter and David! - Original Message From: Peter Ehlers ehl...@ucalgary.ca To: David Winsemius dwinsem...@comcast.net Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org Sent: Wed, May 19, 2010 8:45:24 PM Subject: Re: [R] colored venn diagram

Re: [R] Concatenation

Still not clear. Follow the posting guide and some examples always help. Not sure how you concatenate numbers? You can try, for example, apply(df[1:10,], 2, paste, collapse= ) but this will turn everything into strings. Is this what you want? ..Tao - Original Message From:

Re: [R] save in for loop

Ivan, Try this: eval(parse(text=paste(save(file, i, , file=\file, i, .RData\), sep=))) ...Tao - Original Message From: Ivan Calandra ivan.calan...@uni-hamburg.de To: r-help@r-project.org Sent: Wed, May 19, 2010 7:56:44 AM Subject: [R] save in for loop Dear users, My problem

[R] colored venn diagram

Hi list, This is probably too much to ask, but I'm wondering if there is a ready-to-use function somewhere that allows me to color one area of a venn diagram (e.g. the intersection of two sets)? Thanks! ...Tao __ R-help@r-project.org mailing list

Re: [R] automate curve drawing on nls() object

I can't directly answer your question regarding 'expression', but can you just replace b, c,d, and e with coef(obj)[1], coef(obj)[2], ... etc. You still can automate the whole process this way, right? - Original Message From: array chip arrayprof...@yahoo.com To:

Re: [R] automate curve drawing on nls() object

Subject: Re: [R] automate curve drawing on nls() object well, this is not going automate enough because you have to know how the model (formula) looks like, and how many parameters there are in the model beforehand to do what you are suggesting. Thanks --- On Tue, 5/18/10, Shi, Tao

Re: [R] SAS for R-users

Thomas, If you're thinking to leverage your R programming skill in learning SAS, you'll be disappointed, as the two have quite different grammar. The book Erik mentioned is a good start. After that, just reading the SAS help file, which is pretty comprehensive, will keep you busy. ...Tao

[R] rpart: how to use each variable only once?

Hi list, Is there a way in rpart to force the variables only used once when doing the splits? This is how the question came about. Often time, the tree constructed uses the same variable (say X1) for the first and second splits, for example. However, due to practical reason, the researcher

Re: [R] Multiple plots; single x(y) labels

Gurmeet, I think Xin is more interested in the common axes, rather than just one single xlab or ylab. Jim's solution is much more fancier than mine :-) ...Tao - Original Message From: Gurmeet r.emailing.l...@gmail.com To: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org

Re: [R] Putting 6 graphs on one page

Without the actual data, it's hard to see what's going on here, but It seems you have to restructure your data object to a long table, then it should be easy to use 'dotplot' to generate your plots. ...Tao - Original Message From: Dimitri Liakhovitski

Re: [R] Multiple plots; single x(y) labels

ha, I was focusing on the wrong thing! Sorry, Gurmeet. Good job! From: Xin Ge xingemaill...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: Gurmeet r.emailing.l...@gmail.com; Jim Lemon j...@bitwrit.com.au; r-help@r-project.org Sent: Fri, May 14, 2010 10:51:26 AM Subject: Re: [R] Multiple

Re: [R] rpart: how to use each variable only once?

This is just one single decision tree, not forest. If you're asking what package I use to construct one single tree, it's 'rpart'. From: Changbin Du changb...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Fri, May 14, 2010 12:35:20 PM Subject: Re: [R] rpart: how

Re: [R] Whiskers on the default boxplot {graphics}

, as I stated earlier. With all these being said, this is up to the R core team to decide. ...Tao - Original Message From: Robert Baer rb...@atsu.edu To: Shi, Tao shida...@yahoo.com; Peter Ehlers ehl...@ucalgary.ca Cc: R Project Help R-help@r-project.org Sent: Thu, May 13, 2010 7:25

Re: [R] a question about latex in Hmisc

directory. So when YAP was called, it was looking for the .dvi file in the R temp folder. Therefore, the error window. http://i41.tinypic.com/15qz387.jpg I wonder how to fix that? Thanks! ...Tao - Original Message From: Duncan Murdoch murdoch.dun...@gmail.com To: Shi, Tao

Re: [R] a question about latex in Hmisc

f.harr...@vanderbilt.edu To: r-help@r-project.org Sent: Wed, May 12, 2010 4:28:20 PM Subject: Re: [R] a question about latex in Hmisc On 05/12/2010 03:33 PM, Shi, Tao wrote: Hi Ista, Thanks for the reply! You actually misunderstood me. I never objected the tmp- latex(x) method (in fact

Re: [R] Path to R script

In this case, deploy them as a R package is the way to go. - Original Message From: Johannes W. Dietrich j.w.dietr...@medizinische-kybernetik.de To: Shi, Tao shida...@yahoo.com; johannes.dietr...@rub.de Cc: r-help@r-project.org Sent: Thu, May 13, 2010 9:14:24 AM Subject: Re: [R

Re: [R] Multiple plots; single x(y) labels

Not sure why you want to do that b/c this can be done with one function call of xyplot in lattice. Anyway, you can always set axes=F and then replot each axis using 'axis' for each plot. Make sure before you do that, set your xlim and ylim, so all four plots have the same xlim and ylim. Like

Re: [R] read table for Fisher Exact

Hi Prof. Harrell, Could you please elaborate on why chi-square test is more appropriate in this case? Thank you very much! ...Tao - Original Message From: Frank E Harrell Jr f.harr...@vanderbilt.edu To: r-help@r-project.org Sent: Thu, May 13, 2010 5:35:07 AM Subject: Re: [R]

Re: [R] read table for Fisher Exact

Thanks, David! - Original Message From: David Winsemius dwinsem...@comcast.net To: Frank E Harrell Jr f.harr...@vanderbilt.edu Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org Sent: Thu, May 13, 2010 8:29:31 PM Subject: Re: [R] read table for Fisher Exact On May 13, 2010

[R] a question about latex in Hmisc

Hi list, Excuse me b/c this is probably a more TeX then R question. I've been using latex function in my .Rnw file to generate tables, but I've always been using it without assigning the result to a object, i.e. x - matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','this that')))

Re: [R] Whiskers on the default boxplot {graphics}

Jason, All these are clearly defined in the help file for 'boxplot' under 'range'. Don't understand how you missed that. ...Tao - Original Message From: Jason Rupert jasonkrup...@yahoo.com To: Dennis Murphy djmu...@gmail.com Cc: R Project Help R-help@r-project.org Sent: Wed,

Re: [R] a question about latex in Hmisc

. It actually worked for me once (i.e. I got Yap poped out to preview the table I'm generating), but I had no idea what I did differently. ...Tao - Original Message From: Erik Iverson er...@ccbr.umn.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Wed, May 12

Re: [R] a question about latex in Hmisc

. Heiberger r...@temple.edu To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Wed, May 12, 2010 12:34:13 PM Subject: Re: [R] a question about latex in Hmisc Shi, Tao wrote: so, I always get the error window (attached) poped out. The image was stripped by the mailer. Please type

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