similar to: conf int mixed effects

Hi, concerning my earlier mail, maybe someone has noted from the variable names that I try to analyse mircoarrary experiments. Does anybody know of a R-implementation of the two-step mixed-model normalization procedure proposed by Wolfinger et al. (2001) J. Comput. Biol. 8:625-637? That would be great, best, joerg

Hi, I have the following linear mixed model: y(g,i,j,k,l)=u + L(g) + T(i) + D(j) + S(k) + (TS)(i,k) + error(g,i,j,k,l) where S(k) and the combined effect (TS)(i,k) are random effects whereas the rest are fixed effects. How do I specifiy the random part of the model formula in lme(), especially concerning the combined effect (TS)? Moreover, when I run the model as a fixed effect model I get

Hi, does anybody know of a nice test to detect trend turning points in time series? Possibly with reference? Thanks, joerg

Hi, trying to do a robudt regression of a two-way linear model, I keep getting the following error: > lqs(obs ~ y + s -1,method="lms", contrasts=list(s=("contr.sum"))) Error: lqs failed: all the samples were singular Robust regression with M-estimators works (also regular least square fits, of course): rlm.formula(formula = obs ~ y + s - 1, method = "M",

Hi, I am trying to create a R-package. When I load my R source files using source() for debugging reasons everthing works fine and all function also do want they are supposed to do. However, when I run 'R CMD check' it stop with * checking R files for syntax errors ... ERROR Syntax error in file Is there a way to further investigate where the error is? greetings, joerg

Hi, I have two non-normal distributions and use interquartile ranges as a dispersion measure. Now I am looking for a test, which tests whether the interquartile ranges from the two distributions are significantly different. Any idea? Thanks, joerg [[alternative HTML version deleted]]

Dear R-Users I have the following matrix > out$desc [,1] [,2] [1,] "" "" [2,] "y_{01}(k-001)" "" [3,] "y_{01}(k-002)" "" [4,] "y_{01}(k-003)" "" [5,] "u_{01}(k-001)" "" [6,] "u_{01}(k-002)" "" [7,] "u_{01}(k-003)" ""

Dear List, is there an elegant (or even not elegant) way how to transform dissimilarity or distance matrix A (or, in general, arbitrary symmetrical matrix) by transposition of rows and columns into a form closest to "block diagonal" matrix B? The matrix A is adjusted the following way A[A<epsilon] <-0 #(epsilon is given "small" number) B: (in its ideal form)

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Hello, Situation: We are in a school class every student logs on with the same account. Until now we had Shares that were accessable for everybody and it was therefore possible to look into and edit/delete other's files. Plan: Create a share that can be clicked on which then asks for User/Pass and directly maps to the User's home Directory upon auth. User auth is done through LDAP

Hi all, I have an interesting one - Solaris uses a lot of commands to configure specific items. A simple example is coreadm. In this example: # coreadm -p "/var/core/core_%n_%f_%u_%g_%t_%p" will set the directory and filename to dump core files (with some expansion). The question is - how to get this to run only if the config has changed. I have come up with 2 options, neither of

Hi, I have problems installing RMySQL under R1.8.1 and RHlinux (kernel2.4.7). During compilation I get: ** libs gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486 -fno-strength-reduce -g -c RS-DBI.c -o RS-DBI.o gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -m486

Hi, I have a levelplot with one panel. I just can't find out how I can manipulate the size of the axis lables. e.g. scales.cex doesn't work, the usual par-parameters either. Any hint? joerg

Hello, I am trying to model an intensity function with time-varying covariates. Before, I have successfully defined a log likelihood function for a Power-Law Process (lambda(t)=alpha*beta*t^(beta-1)) with two paramters and no covariates for a repairable systems with failure times (t). This function was maximized with R optim. No problem! But now I want to include a covariate indicating a

I would suggest the method of Sokal and Rholf (1995) S. 498, using the F test. Below I repeat the analysis by Spencer Graves: Spencer: > df1 <- data.frame(x=1:3, y=1:3+rnorm(3)) > df2 <- data.frame(x=1:3, y=1:3+rnorm(3)) > fit1 <- lm(y~x, df1) > s1 <- summary(fit1)$coefficients > fit2 <- lm(y~x, df2) > s2 <- summary(fit2)$coefficients > db <-

Dear all this is a question of model specification in lme which I'd for which I'd greatly appreciate some guidance. Suppose I have data in long format gene treatment rep Y 1 1 1 4.32 1 1 2 4.67 1 1 3 5.09 . . . . . . . . . . . . 1 4 1 3.67 1 4 2 4.64 1 4 3 4.87 .

rkotler at mipsswbrd006-le:~/caviumllvm/build/test$ make Making LLVM 'lit.site.cfg' file... Making LLVM unittest 'lit.site.cfg' file... ( ulimit -t 600 ; ulimit -d 512000 ; ulimit -m 512000 ; ulimit -s 8192 ; \ /usr/bin/python /home/rkotler/workspace/llvm/utils/lit/lit.py -s -v . ) XPASS: LLVM :: tools/llvm-cov/llvm-cov.test (8916 of 9784) ******************** TEST

Hi, I wonder if there is a possibility to avoid that R sets one level of a factor equal zero in a model fit. More precisely, I want to fit a two-way unbalanced linear model: o ~ 0 + x + y x is a factor with 10 levels, y is a factor with 9 levels. In order to get a unique solution i set the intercept =0 and impose that sum(y)=0 i.e. res <- lm(o ~ 0 + x + y,

Hi, I am running the 64bit version of R on a AIX RS6000 cluster on which is also running the ' SQL*Plus: Release 9.2.0.2.0' in the 'ORACLE-environment Version 64 bit AIX 5.1'. I have problems setting up an Oralce database connection. I can instantiate a driver using drv <- Oracle(). But when I try to connect to my database using dbConnect (dbConnect(drv,

Hi, I recently wrote a new R package, which I could 'R CMD check' and 'R CMD build' nicely on my Intel Linux PC. Loading the new library as a normal user on my PC also works nicely. This packages includes some compiled C-code in a shared library. However, before submitting the package to CRAN I wanted to install it also under an other platform in order to check if everything