similar to: vectorizing ANOVA over a vectorized linear model

I'm having trouble with a Bioconductor package, an variable expected in an environment does not seem to be there. As part of my investigation of the problem (most likely on my end) I'd like to list the variables contained in an environment. If you have an environment loaded, lets call it "pkgEnv', how does one find what it does contain? Mark

I have a very long list of strings. Each string actually contains multiple values separated by a semi-colon. I need to turn each string into a vector of the values delimited by the semi-colons. I know I can do this very laboriously by using loops, nchar, and substr, but it is terribly slow. Is there a basic R function that handles this situation? If not, is there perhaps a faster way to do it than

I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark > sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu locale:

I just downloaded R-devel and when loaded it immediately segfaults. I'm not sure how much or what sort of diagnostic info and can provide, but below is my build script, my console output, and the output of uname -r. I am currently dependent on the development version of a package, so I'd like to get R-devel up and running if possible. I am sure there is more info I can provide, but before

I'm having trouble achieving the results I want using a regular expression. I want to eliminate all characters that fall within square brackets as well as the brackets themselves, returning an "". I'm not sure if it's R's use of double slash escapes or something else that is tripping me up. If I only use one slash I get 1: '\[' is an unrecognized escape in a

I need to write a table that can be opened in Excel or OpenOffice such that there are newlines embedded within cells. After much Googling and futzing, I can't figure out how to do this. The way to do this within Excel is alt-Enter and I've tried '/n', '/n/r', '/r/n' per some web suggestions without luck. Anybody know what character or ASCII code to use for this?

For years I have been using options(error = recover) either in .Rprofile or from within R for debugging purposes. The functionality of this appears to have changed and I can't recover it (no pun intended) using the ?options help page. How can I get the old functionality back, particularly from within .Rprofile? A specific line entry would be appreciated. An example, the help page, and

I have fit a model to ~20k different genes and would now like to extract the p-val for one of the effects, again for each individual gene. My model code is: mod <- lm(myResponseMatrix~ Time) Were I to do this with a response vector rather than matrix, the following would work: anovaResult<- anova(mod) With a more complex lm object, such as that generated above, it seems anova is trying to

I have a very long list that I'd like to subset based on a logical value within each element. Example below. I'd like to get just those list elements for further study whose $sig.cor slot is TRUE. In this example, I'd only want element [[2]]. Should be simple, I know. How can I do this? Thanks, Mark > gene.pair.tf.lst [[1]] [[1]]$gene.pair [1] "Lgals1:Pxmp2"

I am performing many permutations on a data-set with each permutation producing a variable number of results. I thought that the best way to keep track of all this in one object would be with a list ('res.lst'). To address these variable results for each permutation I attempted to construct this list using 'assign'. There is even more nesting than indicated below, but this is a

I am analyzing an experiment in which time is a factor, represented by numbers indicating time since last treatment, but in this particular case there is no reason to think that time has a numeric meaning in the sense that 24 would be greater than 6. We have no idea which genes will be increasing or decreasing at different times. So I have the following model (to be applied over many genes): mod

I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected")) most.between.vert <-

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Subject pretty much says it all. Wonder if there is there is some code in XML that the new gcc doesn't like? See output below: * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking

I'm trying to use mtext to create a main title over multiple plots. Below is a simple self-contained example and my sessionInfo (I should note I've also tried this with R-2.8.1 with the same results). When I execute the code chunk below, I get the plots, but no title. I've tried this using the screen driver, pdf, and postscript. I've used different sizes of paper. I suspect I am

I have an example where escaping "." does not seem to be behaving consistently, but perhaps it is due to my misunderstanding. Could someone explain to me why the below produces the output it does? It seems to me that in the second example, where I am being more precise about specifying that a "." (dot) should be between the numbers, should produce the same output as the first

I can compile RSPython without difficulty, been when I try to load it, I get the error messages below. Also below are some cryptic warnings I get on R boot (in case these are pertinent) and my sessionInfo(). Any help is appreciated. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for "conditional", package

I would like to create a 3d scatterplot that is interactive in the sense that I can spin it on its axes to better visualize some PCA results I have. What are the options in R? I've looked at RGL and perhaps it will suffice but it wasn't apparent from the documentation I found. Any demo scripts available for a package that will work? Mark -- Mark W. Kimpel MD ** Neuroinformatics **

I'm making some plots on the same page and would like to include an overall title instead of individual main titles as they are similar and their x and y axis labels are sufficient to distinguish them. Is there a way to assign an overall "main" to this page of plots? Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032

I'm having trouble using split on a very large data-set with ~1400 levels of the factor to be split. Unfortunately, I can't reproduce it with the simple self-contained example below. As you can see, splitting the artificial dataframe of size ~13MB results in a split dataframe of ~ 144MB, with an increase memory allocation of ~10 fold for the split object. If split scales linearly, then my