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2. View entire image (full scale) (Alt F) 3. Undo (limited in utility, be careful! ... (reverses zoom-ins step by step) (Alt Z) 5. Block mode (used during ...
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grid-geometry - # of replicate fields, grids, rows/grid, columns/grid ... Grid-coordinates are specified the same as for GIPO file ...
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... all spots, e.g. the fifth percentile of all the spot intensities, or the ... g. GenePix uses all non-foreground pixels within 3d of the center of the spot, ...
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Title: MicroArray Image Analysis Author: Robin Liechti Last modified by: Carol Bult Created Date: 2/22/2002 1:15:29 PM Document presentation format
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... mG oI jD hB lH lD rM oI pI kC nF qI rM tN xT uM vQ pH tM rI xQ tL vN {U xQ ... w z t w } y | x {} w { z ' } ' ' ~ ' p S ...
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Facility for Genomics and Proteomics and UFSNBN Bioinformatics Node
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DNA Sequencing and Analysis ... increase engagement of undergraduates in research ... Nanodrop ND-1000 uv-vis spectrophotometer. Original Timeline. June 2006 ...
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Other uses of DNA microarrays
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And a few million dollars of computer equipment! Dynamic Graphics: ... Kara Swanson, Katarina ... worst of Statistical Graphics. www.math.yorku.ca/SCS/Gallery ...
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CS491JH: Data Mining in Bioinformatics Introduction to Microarray Technology Technology Background Data Processing Procedure Characteristics of Data
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2. Select separate GIPO file if needed using the 'Browse GIPO file' . 2.1 Repeatedly select 1 or more input files using the 'Browse input files' ...
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Two Color Microarrays
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Affymetrix vs' glass based arrays
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Microarray Image Processing
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Foreground and background intensity are determined from the histogram of pixel ... Spot's measured intensity includes a contribution of non-specific hybridization ...
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Microarray is a tool for analyzing gene expression that consists of a small ... mer oligonucleotides in conjunction with Operon Qiagen based on the TIGR Maize Database ...
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From Peter McCallum Cancer Research Institute, Australia. Normalisation - print tip ... David Freedman. CSIRO Image Analysis Group. Michael Buckley. Ryan ...
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... amount of data resulting from the scanning of two images (one red, one green) ... PS2PDF public domain postscript to PDF converter ...
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Comparative Genomic Hybridization Srikesh G. Arunajadai Division of Biostatistics University of California Berkeley PH 296 Presentation Fall 2002
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P-value is the probability of observing as extreme or more ... Randomly is the key word here that allows us to ascribe observed changes to the treatment alone. ...
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Composite Image file (optional, most often .jpeg files). Gene Array List (.gal) file (optional) ... Re-order arrays within a project ...
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Laboratory. of Molecular Technology. Laboratory of Molecular Technology (LMT) ... Diagnostics-Kris Pike. Oligonucleotide synthesis- Leo Lee ...
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Download normalised M values (txt file) Microarray Data Flow at TIGR. Image Analysis ... Requires Java Runtime environment and Windows XP. MIDAS data analysis methods ...
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The Genome Access Course Microarray Informatics
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Mesure des niveaux d'expression des gnes chez les bactries par la technique des biopuces Analyse du
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3.2 you may 'Assign GIPO fields' in user data file ... 7. Optional 'Save Layout' to Array Layout Database After Edit Layout and Assign fields ...
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National Center for Biomedical Computing at
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default = print-tip loess ... because: loess normalization doesn't affect the A-values ... but no correction (e.g. normexp) or loess!!! Linear models. design matrix ...
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All the genes you want' Label cDNA. from sample 1 RNA ...and sample 2 ... Agamous (y) petal. Petals, pedicels. Carpels, siliques. Tertiary Analysis (Clustering) ...
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One base at a time. Uses process of photolithography. Developed for printing ... Composition based on design rules. Empirically derived. Photolithography ...
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John Powell, Chief, BIMAS, CIT. 5. Architecture for Array Informatics. Central. Expression ... The process is iterated until the group compositions converge. ...
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Department of Statistics, University of California, ... Transfer to Oak Ridge phenol resistant centrifuge tubes. 3. Add 800 ul 25% SDS, 12 ml acid phenol. ...
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Introducing the mAdb system
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Ligate together the oligomers and clone them. Sequence thousands of clones. ... Ligate, PCR, and gel purify ditags (102bp). Recleave with anchoring enzyme ...
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2. base file name of quantification file (without .quant file extension) ... Quant data - assigns names of quantified data in the user file to MAExplorer ...
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Microarray data (scanned image data of expressed genes) are obtained from ... The oncology field has been especially active and to an extent successful in ...
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2. Select separate GIPO file if needed using the 'Browse GIPO file' . 2.1 Repeatedly select 1 or more input files using the 'Browse input files' ...
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Objective: Motif discovery and use for deriving biological information ... Genome wide functional analysis using motif to find biological pattern ...
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Comparative genomic hybridization allows a comprehensive analysis of multiple ... Density of hybridizable DNA that is bound to the Spot ...
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Intensity extraction (for each spot) Foreground fluorescence intensity pairs (R, G) ... Spot Picking. Classification of pixels as foreground or background ...
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Sequence Analysis & Gene Expression Organism selection: genome size why what is the benefit - politics Decisions: mapping first, shotgun sequencing , BAC ...
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Gene expression levels correspond to protein levels ... Precipitate Locally low signal Comet-tails (donut hole) Two Types of glass- microarrays ...
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It is a GNU project which is similar to the S language and environment which was ... Promote high-quality documentation and reproducible research. ...
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Transcriptomics applied to Obesity
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REMBRANDT Empowering Translational Research REpository of Molecular BRAin Neoplasia DaTa HL7 Clinical Genomics SIG Atlanta, September 04 Agenda Translational ...
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MAGE. Computer standard. A standard 'object model' for Microarrays ... MAGE-ML. A collection of these objects in an XML format ...
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1. Select the Chip Set array layout (Scanalyze) if in list, ... 2. Selecting Scanalyze Chipset Array-Layout. 3.1 Select GIPO Input File with 'Browse GIPO file' ...
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http://puma.princeton.edu/help/ http://puma.princeton.edu/help ... The names should be separated by two colons. Gene Selection: All genes. Ten arrays. All genes ...
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madb-support@bimas.cit.nih.gov ... Use web site: http://madb-training.cit.nih.gov. Avoid maximizing web browser to full screen. ...
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Jeff Trent. CIT NCI mAdb. John Powell, Chief, BIMAS. Liming Yang, Ph.D. Jim Tomlin ... Tammy Qiu, SRA. INTERNATIONAL, INC. 58. 59. Averaging Arrays ...
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Analysis of Large Scale Gene Expression Data
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Knock-outs and wild types. Cancer vs normal samples. Time course ... Detection of patterns for both genes and samples. Good visualization with tree graphs ...
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For each gene that is a target for the array, we have a known DNA sequence. ... Quantile normalization makes the overall distribution of intensity values across ...
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ArrayDesign - Describes the design of an gene ... Development cycle may be too short. caGrid software made the installation process very easy, but not ...
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