search for: geneticists

...be 5.30E-16 by a colleague and 5.2974E-16 from SAS. I tried to get around with mvtnorm package but it turns out to be using pnorm for univariate case. I should have missed some earlier discussions, but for the moment is there any short answer for a higher precision? Somehow these days, statistical geneticists are infatuated with such tiny p values! Many thanks in advance, Jing Hua _________________________________________________________________ Telly addicts unite! [[alternative HTML version deleted]]

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

I'm attempting to compile and install R version 1.7.1 for my statistical geneticists. It seems to compile correctly -- that is, it compiles without errors -- but the regression test is failing in the following manner: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > ## log > stopifnot(all.equal(log(1:10), log(1:10, exp(1)))) > stopifnot(all.equal(log10(30), log(30, 10)))...

Hello, I am trying to compile the R package on a sun. I get the error message rbitmap.c: In function 'my_png_error': rbitmap.c:73: structure has no member named 'jmpbuf' rbitmap.c: In function 'R_SaveAsPng': rbitmap.c:122: structure has no member named 'jmpbuf' make[4]:*** [rbitmap.lo] Error 1 Has anyone encountered this problem? Any solutions? Is there are

Hi, I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but I keep getting memory errors. Can somebody please help me with this. Or is therea remote server I can send my data to for computation? Any help is much appreciated. Thanks Dr. Tristan Coram Postdoctoral Research Associate Research Plant Pathologist/Geneticist United States Department of

Dear All, How to cite the PDF user's guide for the LIMMA package? This is not about how to cite the LIMMA package. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov

Hi I am sure there is a function out there already but I couldn't find it. I have SNP data, that is, a matrix which contains in each row two characters (they are different in each row) and I would like to convert this matrix to a binary one according to the minor allele frequency. For non-geneticists: I want to have a binary matrix for which in each row the 0 stands for the less frequent character and 1 for the more frequent character. Thanks for any suggestions. Hadassa -- Hadassa Brunschwig PhD Student Department of Statistics The Hebrew University of Jerusalem http://www.stat.huji.ac.il

Hi Martin, In using the Cluster Package, I have results for PAM and DIANA clustering algorithms (below "part" and "hier" objects): part <- pam(trout, bestk) # PAM results hier <- diana(trout) # DIANA results GeneNames <- show(RG$genes) # Gene Names are in this object But

Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL,

In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware. This is the R script: library(nlme) treat=as.factor(c(1,2,1,2,1,2,1,2)) mouse=as.factor(c(1,1,2,2,3,3,4,4))

All- Does anyone on the list have experience with building RODBC from source on a Linux box for use with DB2? I am using (all from source): R 2.0.1 unixODBC 2.2.9 RODBC 1.1-3 For example: [jcole]$ R CMD INSTALL RODBC_1.1-3.tar.gz 2> rodbc.log * Installing *source* package 'RODBC' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether

...on model selection (occasionally, I'm able to exhaustively compare all possible models, but usually it is done by forward-backward algorithm). I'm OK with this so far. The use of step() seems fairly standard. But now here's where I think it gets weird: There is a compulsion among geneticists to then treat the results of the stepwise model selection as yet a fourth analytical tool by which to rank all the mapping markers, i.e., as further evidence that a marker must be near a genetic element affecting the trait. "If it's included in the model, it must be close to a genetic eff...

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a

...ses/functions wrapped by SWIG as Python libraries. R is used extensively as plotting and statistical analysis engine through RPy package. I use Python to wrap simuPOP since most the following can be easily done using SWIG or Python C API. However, since Python is less used by bioinformaticists and geneticists, I am asked again and again why I do not wrap simuPOP with R (R is also OOP etc...). Although I am a long time R user, I am not familiar with package writing in R. From what I read from R website, it is easy to wrap individual C/C++ functions but not C++ classes. Can anyone take the time to review...

...datasets (e.g., expression profiling, and other ?omics? sets). In this role, he/she will share accountability for achieving team goals focused on: * Drug target discovery * Early biomarker discovery * Pathway understanding and mechanistic insight Teams will consist of computational biologists, geneticists, statisticians and bioinformatics specialists. These statistician positions are unique in requiring a substantial working knowledge of biology. This is necessary in order to collaborate effectively with biologists in the design of appropriate experiments that will effectively elucidate the biolo...

-------- Original Message -------- Subject: [AGDG-LIST:428] Summer Course in Guelph Date: Fri, 22 Dec 2006 09:12:24 -0500 From: Larry Schaeffer <lrs at uoguelph.ca> Reply-To: lrs at uoguelph.ca To: Animal Geneticist's Discussion <agdg-list at colostate.edu> The Centre for Genetic Improvement of Livestock at the University of Guelph is pleased to announce a one week summer course

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-