search for: metabolom

Hi everybody, I am a beginner in the steps of pre-processing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in R repositories? Many thanks in advance. Best regards, Núria ------------------------------------------------------- Núria Queralt Rosinach, Ph.D...

...R/system command line interface but I thought there may be a simpler way to do this through R. Many thanks, Gavin. Dr. Gavin Blackburn SULSA Technologist Strathclyde institute of Pharmacy and Biomedical Science 161 Cathedral Street, Glasgow. G4 0RE Tel: +44 (0)1415483828 ScotMet: The Scottish Metabolomics Facility www.metabolomics.strath.ac.uk<http://www.metabolomics.strath.ac.uk> [[alternative HTML version deleted]]

...f 8 and hope that a large number of those are good data sets so I have an aid to identify bad sets. Thanks, Gavin. Dr. Gavin Blackburn SULSA Technologist Strathclyde institute of Pharmacy and Biomedical Science 161 Cathedral Street, Glasgow. G4 0RE Tel: +44 (0)1415483828 ScotMet: The Scottish Metabolomics Facility www.metabolomics.strath.ac.uk<http://www.metabolomics.strath.ac.uk> [[alternative HTML version deleted]]

...ated in Innsbruck, Austria, has an opening for a biostatistician. If you have any interest, feel free to contact me or Dr Markus Speiser (markus.speiser*at*biocrates.com). Best regards, David ################## Biostatistician (m/f) Job Description BIOCRATES Life Sciences AG is a leading metabolomics company using a mass-spectrometry based technology platform. Its products and services extract, deliver, and present rich information residing in metabolite networks with unprecedented speed, low cost, and high reliability. Biocrates? quantitative approach enables immediate identification of met...

Dear R Users, I have a network of 25000 total nodes and a list of 500 node which is a subset of all nodes. Now I want to calculate the APSP (all pair shortest path) matrix only for these 500 nodes. I would appreciate any help. Thanks in advance Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]]

Dear R users, I have a matrix like A X 1 B Y 2 C Z 3 I want to reshape this matrix into this format X Y Z A 1 B 2 C 3 Thanks in advance for your help. Dinesh -- Dinesh Kumar Barupal Junior Specialist Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]]

....00 .67 00 00 96 .00 .87 00 00 Where first column represent the Variable name. And if the first matrix is transposed, then how to get the output in which First raw present the variable name. It will be great help for my research. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]]

...7 8 9 2 3 I want to reshape the matrix in this format Row Col Value a D 4 a E 5 a F 6 . . .. e E 9 I want only the pair which pass a threshold for example >3. Please help me. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]]

...t a child matrix from above with specific row names or col names. e.g. For above matrix I need only rows which has following row names. 5951 236 6306 5950 145742 1123 I would appreciate if you can use this matrix as input. Thanks in advance. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[alternative HTML version deleted]]

...The chosen candidate will be part of ourmultidisciplinary team conducting studies to discover and developdiagnostic biomarkers as well as biomarkers for the characterization ofdisease models and drug effects ? including side effects. Essential functions * Analyzing omics data and integration of Metabolomics with other omics data-selection of likely metabolite, protein and RNA targets for quantification. * Providing software support for team members. * Contributing to presentations, patent applications, scientific publications and reporting on project funding. Requirements * Candidate can work ind...

L.S. OpenAnalytics is an international company providing data analysis services and products across geographies and industrial sectors. We are currently looking to extend our team with the following profile Data analyst: MSc / PhD in molecular or computational biology having a keen interest in data analysis A detailed description can be found at http://www.openanalytics.eu/jobs Strong R

We're pleased to announce that Henning Redestig finally implemented ESS support for Roxygen: http://www.metabolome.jp/download/ess-roxy/ess-roxy.el/view ess-roxy includes paragraph fill, hiding, template generation, etc.

...pril 2009 Number of Pages: 368 Emphasizing the search for patterns within and between biological sequences, trees, and graphs, this book shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions o...

...er des erreurs library(MASS) #Chargement des Librairies library(car) library(Hmisc) library(tkWidgets) library(svDialogs) library(multtest) library(nlme) #Rep <- "C:/Documents and Settings/U3M/Bureau/steph/Scripts R/" Rep <- "C:/Documents and Settings/rafa/Mis documentos/metabolomics/Scripts R/Mod?les Mixtes/" # Choix du fichier ? traiter source(sprintf("%sinfile2bis.q",Rep)) para<-infile2bis() # Ouvre une petite interface permettant de s?lectionner le fichier # que l'on veut traiter Fic <- para$fichier # fic est le fichier ? traiter...

...gularized CCA and sparse PLS to unravel relationships between two heterogeneous data sets of size (nxp) and (nxq) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, mixOmics can also be applied to any other large data sets where p+q>>n. rCCA is a regularized version of CCA to deal with the large number of variables. sPLS allows variable selection in a one step procedur...

CRAN (and crantastic) updates this week New packages ------------ * disclapmix (0.1) Maintainer: Mikkel Meyer Andersen Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen License: GPL-2 http://crantastic.org/packages/disclapmix disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. * EstSimPDMP (1.1) Maintainer: Unknown Author(s):