similar to: Limma - 2x2 factorial design matrix

Hi, I'm using rw2000dev.exe (Win32) built on August 14. If this isn't already planned, can I suggest that when checkS3methods() (called by R CMD check) fails because of a syntax error in a dependent package listed in the DESCRIPTION file of the main package being checked, it would be nice if checkS3methods() reported which dependent package caused it to fail? Running R CMD check on my

Hello, In limmaGUI, after running a linear model for a single gene & time point (mutant vs control), the venn-diagram for differentially expressed genes with a p-value cut-off gives a different number than the top-table with the same cut-off (2600 vs. 791). I have seen the same thing happen before for multiple time points (when the venn-diagram is more relevant) Any ideas what is going on?

Full_Name: Edoardo Giacopuzzi Version: 2.0.1 OS: Windows XP Home Submission from: (NULL) (80.181.65.157) I have some problem with this new version of R GUI. I've used limmaGUI package with an older version of R and it works perfectlly, but now with the last version R 2.0.1.0 two error boxs appear every time I try to launch this package: 1. <<Error in list.files(path, pattern,

[PLEASE REPLY _OFF_ THE LIST, i.e. DON'T CC to r-help at ...] Hi, I don't see this sort of thing very often on the mailing lists, so list moderators and others should feel free to tell me if it breaches list etiquette and/or delete my post if necessary. But I can't see what harm it could do... I am just wondering approximately how many people use / have used some of the R stuff

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Dear R-helpers, I have installed the latest version of R 2.1.1 in the Tiger OSX. However, when I load up R and use the following command: > library(tcltk) I encounter the following error: Loading Tcl/Tk interface ... Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/tcltk.so':

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

I am the maintainer of a Bioconductor package (affylmGUI) which uses tcltk. It freezes inconsistently on MS Windows, but not Mac or Unix. see details below. After considerable testing I have reduced the problem from a few thousand lines of code to 30 lines! If you paste the following lines of code into an R window: testGUI <- function(){ require(tcltk) MainWindow <-

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Hi all, Does anyone know if an R function for the Mantel-Haenszel chi-square for a 2x2 table exists? I’ve also seen it called the randomization Q statistic. Note that I’m not looking for the Cochran-Mantel-Haenszel…I did see that out there as cmh.test. Thanks in advance, Jeff Internal Virus Database is out-of-date. Checked by AVG Free Edition. 11:27 AM [[alternative HTML version

Dear Listers: I have a categorical feature selection problem for random forest. Suppose I have a multiple-leveled category variable A, which has m=3 levels: red, green, and blue and the final target is binary classification. I want to evaluate its power in discrimination between 2 classes. We know rf splits multiple-leveled category variable by considering all combinations of its levels. So

Hello R-users, I would like to generate two-way contingency tables with zero in one cell. I tried to use the function r2dtable but I could not force one cell to have zero value. Any Idea? Best regards.. Mahmoud [[alternative HTML version deleted]]

I wan't a test for the 'association' between two events, lets say the color of balls picked and the pickers (this is quite a good analogy to my data). I have 200 different pickers P I have 1,000 colors of balls C I have 1,000,000 picks in total I am totally confused about what test to apply and when and why. This is what I *think* I know how many balls each picker

R 2.12 windows 7 I am summary data that I would like to make into a 2x2 table representing counts positive vs. negative counts: 28/289 20/276 My table should look something like the following: group1 group2 Positive 28 20 Negative 289 276 How can a (1) create the 2x2 table (2) run a chi square test on the table? I have tried the following code, but I

Hello. I'm looking for a method to simulate n different 2x2 tables having all the same odds ratio. For example. I need 100 tables with odds ratio 1 100 tables with odds ratio 2 100 tables with odds ratio 3 and so on. All tables should have the same marginal frequencies. Thank you -- View this message in context:

Dear Colleagues, Could you recommend a package of combination of functions in R for analysis of 2x2 tables of various designs. Preferably it should include tests and confidence limits (both exact and approximate) for alternative designs, such as independent proportions (e.g. parallel group clinical trials) and correlated proportions (matched pairs and crossover studies). Many thanks MM

I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? I thought fisher.exact is only for 2x2 tables. Note: I can't use chi-squared because I have a couple of cells with 0 and < 5 observations. -- View this message in context: http://r.789695.n4.nabble.com/fisher-exact-for-2x2-table-tp3481979p3481979.html Sent from the R help

Does anyone know how I can generate a 2x2 table in a format where in each cell of the table, it contains a) count (frequency) b) total percentage c) row percentage d) column percentage. SAS can generate this format easily, is there a R package that can do this? Frequency | Percent | Row Pct | Col Pct | positive negative | Total --------------------------------|------- disease |

Hi, Found no measure of association or correlation for 2x2 contingency tables in fullrefman.pdf or google. Can someone point to a package that implements such calculations? Thanx. -- Alexandre Santos Aguiar - consultoria para pesquisa em sa??de - R Botucatu, 591 cj 81 tel 11-9320-2046 fax 11-5549-8760 www.spsconsultoria.com

Hi, I'm analyzing experimental results where two different events ("T1" and "T2") can occur or not during an experiment. I made my experiments with one factor ("Substrate") with two levels ("Sand" and "Clay"). I would like to know wether or not "Substrate" affects the occurrence probability of the two events. Moreover, for each