Affy PowerPoint PPT Presentations

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Overview of Affy Analysis Pipeline

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Pour r aliser un espace ferroviaire europ en sans fronti res ... Appliquent. Groupes d'experts du secteur. Partenaires sociaux. Organisations de clients. Le ...

'Affy' provides methods for Affymetrix Oligonucleotide Arrays. ... 'Affy' (1/3) ... 'Affy' (2/3) ReadAffy(): read CEL files into an AffyBatch. ...

Aim: ... can examine distribution of relative expressions across arrays. ... Also look at sign of difference. 68. Affy compare probe effects ...

Increase in Prevalence (%) of Obesity Among US Adults ... Imputation method. Illumina 550K. Affy 5.0. Illumina 370. Illumina 370. Affy 6.0. Genotyping Platform ...

For details on reading vignettes, see. the openVignette help page. openVignette() Please select (by number) a vignette. 1: affy primer. 2: affy: Built-in ...

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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Graph coloring register allocation. Alpha and x86 backends. Object-oriented Infrastructure ... Affine partitioning for parallelism & locality unifies: ...

Supports both one- and two-channel data, including affy data ... storing tox parameters, e.g., dose schedule and treatment, sacrifice time, etc ...

form of DNA sequence variation between individuals. The HapMap Project ... SNPs are not the only sequence variation in the genome that can affect primer hybridization ...

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Affymetrix microarray preprocessing and quality assessment. Differential expression ... Affymetrix Microarray Preprocessing and Quality Assessment. Affymetrix ...

R is a language and environment for statistical computing and graphics. ... Other assays: aCGH, DNAcopy, prada, PROcess, RSNPer, SAGElyzer. ...

both array types biased downwards (FC under-estimated compared to qRT-PCR) Evans et al. ... Victor Jongeneel, Christian Iseli, Brian Stephenson. DAF/DAFL. Otto ...

Probabilistic Graph and Hypergraph Matching Ron Zass & Amnon Shashua School of Engineering and Computer Science, The Hebrew University, Jerusalem

an expression platform for gene regulation. A metabolite-binding aptamer domain and Riboswitch Functions U U U U U X 3 4 2 1 Direct (protein-free ...

GROUPEMENT INFRASTRUCTURE. RATP-RFF-SIEMENS-SNCF-SYSTRA. Palais des Congr s. de Strasbourg ... GROUPEMENT INFRASTRUCTURE. RATP-RFF-SIEMENS-SNCF-SYSTRA. Partenaires ...

Distance Weighted Discrimination

Title: Analysis of Affymetrix Microarrays Author: Gareth Palidwor Last modified by: gpalidwor Created Date: 1/18/2005 5:20:25 PM Document presentation format

tool for DNA microarray and ... three major bioinformatics issues are ... An important concept in ArrayTrack Create a gene list through data filtering and statistical ...

Title: How to generate a consensus? Author: Mark Gerstein Last modified by: Mark Gerstein Created Date: 9/21/2005 11:43:10 PM Document presentation format

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Human Genome Project (http://genome.ucsc.edu/downloads.html) Gene Ontology Consortium ... Human Genome Project Date built: 28jun2002. URL:http://www.genome.ucsc.edu ...

We can fit a model to the data of each gene after the whole ... Multiplicity adjustments winnow this down so that the number of false positives is smaller ...

Title: PowerPoint Presentation Author: Judd C. Rice Last modified by: Judd C. Rice Created Date: 7/10/2002 4:19:56 PM Document presentation format

Sense and Anti-sense. or PM and MM (old) RMA for SNP chips ... 90% (MPAM) to 98% (CRLMM) called at comparable accuracy on HapMap data ...

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Assessing the need for sequence-based normalization in tiling microarray experiments. ... or other sequence adjustments of expression, unless gene structure ...

mRNA is reverse transcribed to DNA, and if a complementary sequence is on the on ... labeled with a dye that will fluoresce and generate a signal that is monotonic ...

Data Analysis. Quality control data analysis was performed using GCOS, Expression Console 1.1, ... results are no substitute for transcript-level bioinformatics. ...

211 pseudogenes were identified using an updated ... Sequence conservation in rat, mouse and chimp. EST. ENm004. Affymetrix TARs using Oligo-microarray ...

AT version 2 (2002): in-house microarray core facility ... ArrayTrack contains pathways for human (134), rat (116) and mouse (124) ...

A vignette is an executable document consisting of a collection of code chunks ... Vignettes provide dynamic, integrated, and reproducible statistical documents ...

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Create an union of the remaining pseudogenes. ... Has Trans-criptional Evidence (intersects Gencode transcript) From Deyou Z. 17 ...

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Identification and quantitation of mRNAs in a mixed population by generation of ... 1 dna:chromosome. chromosome:NCBIM36:1:4729550:4729591:1 ...

Data generated with new assembly. Fully integrated with ensembl. Pages are extendable & adaptable ... display information with associated gene. FeatureView ...

ANEXdb: An integrated annotation and expression database. Oliver Couture. Sequence. Function ... Both sequence and function annotation can be predicted. Quick ...

But first...some data-massage! Noise: background and cross-hybridization ... transcriptional profile do change in prostate!! 1.5 1 -1.5. testosterone. Dopping X ...

Expression from pseudogene locus (1) putative novel transcript ... Putative novel transcript supported by a single EST with has a polyA site and signal ...

What genes are expressed in my treated cells versus the control? ... Rat Toxicology Chip - 850 genes. CYP450's, Heat Shock proteins. Drug transporters ...

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Polymorphism: a DNA variation in which each possible sequence is present in at ... Zebrafish. Tetraodon. Mosquito. 11 of 25. Caveat ...

... ratios from 4 red-green 8448-clone cDNA arrays hybridised with zebrafish samples. ... zebrafish data. Loess regression. Locally weighted regression. ...

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Detection of differential expression by different Microarray Platforms (spotted ... but RMA quantile normalization for Affymetrix. Platform Comparison Study. Purpose ...

Equilibrium limit, t , gives the 'Langmuir isotherm': Time-dependent solutions. 512 ... Equilibrium Langmuir isotherm. Parameters y0, b, K all probe. dependent ...

It is a GNU project which is similar to the S language and environment which was ... Promote high-quality documentation and reproducible research. ...

A GeneSpring GX window opens. Importing data. Click file import data select 1 CEL file ... Un-check. Use cross-gene error. Creating an experiment. Close ...

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