Re: [R] variable ordering

2012-02-15 Thread Peter Langfelder
On Wed, Feb 15, 2012 at 10:22 PM, arunkumar wrote: > Hi, > > My input is > > x=c("D","A","B") > Y=c("A","B","C","D") > > varorder=which(Y %in% X) > > I'm getting result as  1 2 4 > But i need the result to be 4 1 2 Here's a hint: lookup the function match. Peter

Re: [R] "CV" for log normal data

2012-02-21 Thread Peter Langfelder
On Tue, Feb 21, 2012 at 1:44 PM, array chip wrote: > Hi, I have a microarray dataset from Agilent chips. The data were really log > ratio between test samples and a universal reference RNA. Because of the > nature of log ratios, coefficient of variation (CV) doesn't really apply to > this kind

Re: [R] "CV" for log normal data

2012-02-21 Thread Peter Langfelder
> > Good advice. But perhaps ?mad or some other perhaps robust plain old > measure of spread? The problem is not (lack of) robustness to outliers, the problem is to find genes whose expression variation is small compared to (mean) expression. Trouble is, Agilent throws the mean expression informat

Re: [R] syntaxe problem

2012-02-24 Thread Peter Langfelder
On Fri, Feb 24, 2012 at 3:47 PM, Adel ESSAFI wrote: > Hello, > I want to create 10 dataframe  using a for loop. > I don t know what to do to create 10 different dataframes whose name is > parametrized with variable i. > This syntaxe fails. It create a unique fataframe called dfn. > Any input will

Re: [R] problem with assign and get

2012-02-27 Thread Peter Langfelder
On Mon, Feb 27, 2012 at 9:41 AM, Jannis wrote: > Dear list members, > > > does anyone have an idea why the following construction does not work but > gives the following error message: > > assign('test', array(1:10, dim=c(10,10))) > dimnames(get('test')) <- list(1:10,1:10) > > > Error in dimnames(

Re: [R] kmeans: how to retrieve clusters

2012-02-27 Thread Peter Langfelder
On Mon, Feb 27, 2012 at 3:18 PM, ikuzar wrote: > Hello, > > I'd like to classify data with kmeans algorithm. In my case, I should get  2 > clusters in output. Here is my data > > colCandInd       colCandMed > 1       82                2950.5 > 2       83               1831.5 > 3       1192     289

Re: [R] call object from character?

2012-04-18 Thread Peter Langfelder
On Wed, Apr 18, 2012 at 7:25 PM, chuck.01 wrote: > Let say I have an object (I hope my terminology is correct) a > a <- 12 >> a > [1] 12 > > And "a" has been assigned the number 12, or whatever > And lets say I have a character "call_A" > call_A <- "a" >>call_A > [1] "a" > > What is the function "

Re: [R] Numbers not numeric?

2012-04-20 Thread Peter Langfelder
On Fri, Apr 20, 2012 at 12:44 PM, Charles Determan Jr wrote: > Greetings R users, > > I have a curious problem.  I read in a csv file (subset shown below) as > normal > data=read.table("C:/Users/Chaz/Desktop/test.csv",sep=",",header=TRUE, > na.strings=".") > > However, the numbers from the dataset

Re: [R] lines crosses

2012-04-20 Thread Peter Langfelder
On Fri, Apr 20, 2012 at 2:48 PM, Ben quant wrote: > > Hello, > > If the exact value does not exist in the vector, can I still get at the > intersections? Is there a simple way to do this and avoid looping? Seems > like there would be a simple R function to do this... > > Example: > vec <- c(5,4,3,

Re: [R] Errors Updating Libraries (2.15)

2012-04-24 Thread Peter Langfelder
On Tue, Apr 24, 2012 at 3:05 PM, Rich Shepard wrote: > On Tue, 24 Apr 2012, Rich Shepard wrote: > >>  I'll rebuild R-2.15 and start over. Will post results after doing that. > > >  New build, new repository, same results. > >  Quite the new experience with R, but one I need to quickly put behind m

Re: [R] Usage line in .pdf version of manual is truncated

2012-04-30 Thread Peter Langfelder
On Mon, Apr 30, 2012 at 12:34 PM, Zeeberg, Barry (NIH/NCI) [E] wrote: > I am creating a package, and a rather long usage line for one function > becomes truncated in the generated .pdf manual. Is there a way that I can > prevent that truncation? How long is "rather long"? In our WGCNA package w

Re: [R] Manually modifying an hclust dendrogram to remove singletons

2012-05-24 Thread Peter Langfelder
On Thu, May 24, 2012 at 9:31 AM, wrote: > Dear R-Help, > > I have a clustering problem with hclust that I hope someone can help > me with. Consider the classic hclust example: > >     hc <- hclust(dist(USArrests), "ave") >     plot(hc) > > I would like to cut the tree up in such a way so as to av

Re: [R] linux

2012-05-27 Thread Peter Langfelder
On Centos and most likely other RedHat/Fedora systems, gfortran is contained in the package gcc-gfortran. Install that package before trying to install R. HTH, Peter On Sun, May 27, 2012 at 8:43 AM, ya wrote: > Hi Rich, > > You mean, the R source code package contains the FORTRAN code? I instal

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