search for: geneticist

...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]]

...e 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 combination. Thank you very much in advance. 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 http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version delete...

...efault of FDR=0.0.5 with a less stringent FDR value (0.10, 0.20, etc.) in the "topTable" function. How do I change it? Thanks a lot for the help on the use of "topTable" function from 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 <mailto:roger.vallejo@ars.usda.gov> [[alternative HTML version del...

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)))...

...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 compiled binary somewhere that I could use? Grateful for any help. Richard Richard Kerr, Quantitative Geneticist MMI Genomics Davis, CA 95616 richard.kerr at mmigenomics.com (desk) 530-297-2938

...s (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 Agriculture Agricultural Research Service Wheat Genetics, Quality Physiology & Disease Research 209 Johnson Hall Washington State University Pullman, WA 99163 Office: +1 509 335-1596 Fax: +1 509 335-2553 Email: tcoram@mail.wsu.edu [[alterna...

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 [[alternative HTML version deleted]]

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

...t be an easy task for a good R programmer. I will appreciate very much directions or R code on how to send the PAM and DIANA results to output files including information on genes (Names) per each cluster. Thank you very much. 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 <mailto:roger.vallejo@ars.usda.gov> [[alternative HTML version del...

...singleChannel = FALSE, : No annotation package was specified. Need to use SetAnnotation later ****************************************************************** I will apreciate help to troubleshoot this error. Thank you very much. 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 http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version delete...

...lme.formula(vec ~ treat + time + treat * time, random = ~1 | : nlminb problem, convergence error code = 1 message = singular convergence (7) I will appreciate your help in pointing mistakes in this R script. Thank you very much. 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 http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version delet...

...uot;hdbc" <More gory details available upon request.> Any thoughts would be very much appreciated. I have verified that my unixODBC installation is good by connecting to a datasource and making some successful queries against my DB2 installation. John. -- Dr. John B. Cole, Research Geneticist Animal Improvement Programs Laboratory 10300 Baltimore Avenue BARC-West, Building 005, Room 306 Beltsville, Maryland 20705-2350 Telephone: (301) 504-8665 FAX: (301) 504-8092 E-mail: jcole at aipl.arsusda.gov

...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 ef...

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 biol...

-------- 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 entitled "Animal Breeding Applications Using R" to be given by Bill Szkotnicki and Larry Schaeffer from June 11...

...ontrasts. I would like to extend properly this concept to my experiments. Thank you very much. Roger PS. To avoid you going to the LIMMA User's Guide. I show below the indicated example and R commands used. Please see below. 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 <mailto:roger.vallejo@ars.usda.gov> ********************************...