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limma: Linear Models for Microarray Data PowerPoint PPT Presentation
limma: Linear Models for Microarray Data - 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 ...
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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Identifying Differentially Expressed Genes PowerPoint PPT Presentation
Identifying Differentially Expressed Genes - 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. ...
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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Talk to geWorkbench group PowerPoint PPT Presentation
Talk to geWorkbench group - Information Transfer at the Sequence Level: How a Protein is Made. DNA - RNA - Protein ... Quantile Normalization. Intensity Plots. Contributions to probe intensity ...
Information Transfer at the Sequence Level: How a Protein is Made. DNA - RNA - Protein ... Quantile Normalization. Intensity Plots. Contributions to probe intensity ...
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Other genomic arrays: Methylation, chIP on chip PowerPoint PPT Presentation
Other genomic arrays: Methylation, chIP on chip - Other genomic arrays: Methylation, chIP on chip UBio Training Courses SNP-arrays and copy number Genotyping arrays can detect CNVs Copy numbers from SNP arrays ...
Other genomic arrays: Methylation, chIP on chip UBio Training Courses SNP-arrays and copy number Genotyping arrays can detect CNVs Copy numbers from SNP arrays ...
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Adaptive OnLine Page Importance Computation PowerPoint PPT Presentation
Adaptive OnLine Page Importance Computation - Adaptive On-Line Page Importance Computation. Serge Abiteboul. INRIA. Domaine de Voluceau ... How to getting those web pages. Changing web pages. How to update ...
Adaptive On-Line Page Importance Computation. Serge Abiteboul. INRIA. Domaine de Voluceau ... How to getting those web pages. Changing web pages. How to update ...
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Other%20genomic%20arrays:%20Methylation,%20chIP%20on%20chip PowerPoint PPT Presentation
Other%20genomic%20arrays:%20Methylation,%20chIP%20on%20chip - Calculate medians for Cy3 and Cy5 at high an low betas ... Recalculate betas with new intensities. DIFFERENTIAL METHYLATION. METHYLATION MICROARRAYS ...
Calculate medians for Cy3 and Cy5 at high an low betas ... Recalculate betas with new intensities. DIFFERENTIAL METHYLATION. METHYLATION MICROARRAYS ...
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BioConductor PowerPoint PPT Presentation
BioConductor - A vignette is an executable document consisting of a collection of code chunks ... Vignettes provide dynamic, integrated, and reproducible statistical documents ...
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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ReportingTools: an automated result processing toolkit for high throughput genomic analyses PowerPoint PPT Presentation
ReportingTools: an automated result processing toolkit for high throughput genomic analyses - * Outline ReportingTools introduction and basics ReportingTools and microarray experiments ReportingTools and RNA-seq experiments ReportingTools and knitr ...
* Outline ReportingTools introduction and basics ReportingTools and microarray experiments ReportingTools and RNA-seq experiments ReportingTools and knitr ...
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Maximum Likelihood "Frequentist" inference PowerPoint PPT Presentation
Maximum Likelihood "Frequentist" inference - Maximum likelihood estimates of the model parameters and 2 are numbers that ... Empirical Bayes 'inflates variances' from the low-variability genes ...
Maximum likelihood estimates of the model parameters and 2 are numbers that ... Empirical Bayes 'inflates variances' from the low-variability genes ...
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F PowerPoint PPT Presentation
F - F rpackningsmaterial R varor Process Egenskaper Anv ndning F rpackningsmaterial Papper och Kartong R varor Process Egenskaper ...
F rpackningsmaterial R varor Process Egenskaper Anv ndning F rpackningsmaterial Papper och Kartong R varor Process Egenskaper ...
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Differential gene expression PowerPoint PPT Presentation
Differential gene expression - Gene screening using ROC curves. Identifying differentially expressed genes ... Logs of ratios are symmetric around zero: The average of log(2) and log(1/2) is 0. ...
Gene screening using ROC curves. Identifying differentially expressed genes ... Logs of ratios are symmetric around zero: The average of log(2) and log(1/2) is 0. ...
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Understanding the design matrix in linear models for microarray experiments Natalie Thorne PowerPoint PPT Presentation
Understanding the design matrix in linear models for microarray experiments Natalie Thorne - Many thanks to Terry Speed, Gordon Smyth, Jean (Yee Hwa) Yang, Ingrid Lonnstedt, ... Based on your idea about what is measured in each sample type (in relation to ...
Many thanks to Terry Speed, Gordon Smyth, Jean (Yee Hwa) Yang, Ingrid Lonnstedt, ... Based on your idea about what is measured in each sample type (in relation to ...
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Microarray%20Data%20Analysis%20-%20A%20Brief%20Overview PowerPoint PPT Presentation
Microarray%20Data%20Analysis%20-%20A%20Brief%20Overview - Affymetrix microarray preprocessing and quality assessment. Differential expression ... Affymetrix Microarray Preprocessing and Quality Assessment. Affymetrix ...
Affymetrix microarray preprocessing and quality assessment. Differential expression ... Affymetrix Microarray Preprocessing and Quality Assessment. Affymetrix ...
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Cluster Analysis of Gene Expression Profiles PowerPoint PPT Presentation
Cluster Analysis of Gene Expression Profiles - Identifying groups of genes that exhibit a similar expression ' ... Systematic determination of genetic network architecture, Nat.Genet., 22, (1999) 281-285. ...
Identifying groups of genes that exhibit a similar expression ' ... Systematic determination of genetic network architecture, Nat.Genet., 22, (1999) 281-285. ...
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HIPCAT Meeting PowerPoint PPT Presentation
HIPCAT Meeting - HIPCAT Meeting
HIPCAT Meeting
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Practical demonstration of R and Bioconductor PowerPoint PPT Presentation
Practical demonstration of R and Bioconductor - Weaver mice. Mutation in GIRK2 K channel gene. Lack mature granule cells ... Two mouse strains (WT, MT) Eight hybridizations (arrows) WT P11. WT P21. MT P21. MT P11 ...
Weaver mice. Mutation in GIRK2 K channel gene. Lack mature granule cells ... Two mouse strains (WT, MT) Eight hybridizations (arrows) WT P11. WT P21. MT P21. MT P11 ...
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Introduction to R and Bioconductor BMI 731 Winter 2005 PowerPoint PPT Presentation
Introduction to R and Bioconductor BMI 731 Winter 2005 - R is a language and environment for statistical computing and graphics. ... Other assays: aCGH, DNAcopy, prada, PROcess, RSNPer, SAGElyzer. ...
R is a language and environment for statistical computing and graphics. ... Other assays: aCGH, DNAcopy, prada, PROcess, RSNPer, SAGElyzer. ...
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Pabio590B PowerPoint PPT Presentation
Pabio590B - Pabio590B week 1 Microarrays Overview Design & hybridization Data analysis Overview Experiments you might do Microarray Design RNA Expression Chip Designs ...
Pabio590B week 1 Microarrays Overview Design & hybridization Data analysis Overview Experiments you might do Microarray Design RNA Expression Chip Designs ...
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BioConductor tutorial PowerPoint PPT Presentation
BioConductor tutorial - It is a GNU project which is similar to the S language and environment which was ... Promote high-quality documentation and reproducible research. ...
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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Friday 130 second computer lab session: PowerPoint PPT Presentation
Friday 130 second computer lab session: - Friday (1/30) second ... where is the shrunken estimate of standard deviation. ... We will come back for the selection of a0 later. 2.3. Empirical Bayes ...
Friday (1/30) second ... where is the shrunken estimate of standard deviation. ... We will come back for the selection of a0 later. 2.3. Empirical Bayes ...
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Global Analysis of Functional Units of Plant Chromosomes: PowerPoint PPT Presentation
Global Analysis of Functional Units of Plant Chromosomes: - The mid S-phase profile is also distinct from the late profile (R= -0.85). These data indicate that replication in Arabidopsis is basically a two phase process.
The mid S-phase profile is also distinct from the late profile (R= -0.85). These data indicate that replication in Arabidopsis is basically a two phase process.
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Comparison of gene expression data in different commercial and home spotted platforms: a biological PowerPoint PPT Presentation
Comparison of gene expression data in different commercial and home spotted platforms: a biological - DEGs by Agilent only 8/15. Checks in AGL data. Permutation ... Agilent seems more sensitive in detecting small effects. Acknowledgements. Human Genetic Center ...
DEGs by Agilent only 8/15. Checks in AGL data. Permutation ... Agilent seems more sensitive in detecting small effects. Acknowledgements. Human Genetic Center ...
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Bioconductor PowerPoint PPT Presentation
Bioconductor - Byron Ellis, Department of Statistics, Harvard University, USA. ... Kurt Hornik, Technische Universitat Wien, Austria. ... Technische Universitat Wien, Austria. ...
Byron Ellis, Department of Statistics, Harvard University, USA. ... Kurt Hornik, Technische Universitat Wien, Austria. ... Technische Universitat Wien, Austria. ...
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cellHTS class and workflow components for cellbased assays PowerPoint PPT Presentation
cellHTS class and workflow components for cellbased assays - ... well be applied to the screening of small molecules (compounds) ... Thomas Horn, Tina B chling, Dorothee Nickles. Elin Axelsson. Gregoire Pau. Martin Morgan ...
... well be applied to the screening of small molecules (compounds) ... Thomas Horn, Tina B chling, Dorothee Nickles. Elin Axelsson. Gregoire Pau. Martin Morgan ...
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Canadian Bioinformatics Workshops PowerPoint PPT Presentation
Canadian Bioinformatics Workshops - Canadian Bioinformatics Workshops www.bioinformatics.ca Lecture 8: Microarrays Part II bioinformatics.ca Module 1 bioinformatics.ca multi chip? Why does it assume all ...
Canadian Bioinformatics Workshops www.bioinformatics.ca Lecture 8: Microarrays Part II bioinformatics.ca Module 1 bioinformatics.ca multi chip? Why does it assume all ...
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GBIO001-9 Bioinformatics PowerPoint PPT Presentation
GBIO001-9 Bioinformatics - GBIO001-9 Bioinformatics Introduction
GBIO001-9 Bioinformatics Introduction
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Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIPseq Data PowerPoint PPT Presentation
Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIPseq Data - CisGenome: system to analyse ChIP data. visualization. data normalization. peak detection ... Different ranking methods on the transcriptome data will be analyzed. ...
CisGenome: system to analyse ChIP data. visualization. data normalization. peak detection ... Different ranking methods on the transcriptome data will be analyzed. ...
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Exploring Data using Dimension Reduction and Clustering PowerPoint PPT Presentation
Exploring Data using Dimension Reduction and Clustering - Initialize the K cluster centroids (with points chosen at random) ... Points can move from one cluster to another, but the final solution depends ...
Initialize the K cluster centroids (with points chosen at random) ... Points can move from one cluster to another, but the final solution depends ...
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Data Analysis of Microarrays Bioconductor.org PowerPoint PPT Presentation
Data Analysis of Microarrays Bioconductor.org - CEL files contain information about the expression levels of the individual probes. ... The data is from a study of lipid metabolism by Callow et al (2000) ...
CEL files contain information about the expression levels of the individual probes. ... The data is from a study of lipid metabolism by Callow et al (2000) ...
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SMD Data Quality Assessment and Repository Tools Tutorial PowerPoint PPT Presentation
SMD Data Quality Assessment and Repository Tools Tutorial - Also can be used to compare cDNA prints with h/meebo arrays ... HEEBO/MEEBO plots ... HEEBO/MEEBO: diagnostics. Box-plots for groups of reporters (colors same ...
Also can be used to compare cDNA prints with h/meebo arrays ... HEEBO/MEEBO plots ... HEEBO/MEEBO: diagnostics. Box-plots for groups of reporters (colors same ...
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miRNAs and biomarkers PowerPoint PPT Presentation
miRNAs and biomarkers - miRNAs and biomarkers Gabriella Sozzi * * The MILD trial ..... In this large study the diagnostic performance of the plasma-based miRNA test was retrospectively ...
miRNAs and biomarkers Gabriella Sozzi * * The MILD trial ..... In this large study the diagnostic performance of the plasma-based miRNA test was retrospectively ...
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Prsentation PowerPoint PowerPoint PPT Presentation
Prsentation PowerPoint - Prsentation PowerPoint
Prsentation PowerPoint
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SMD Data Quality Assessment and Repository Tools Tutorial PowerPoint PPT Presentation
SMD Data Quality Assessment and Repository Tools Tutorial - After averaging: - a new row for the synthetic gene data ... during averaging) - Can have comment lines (start with #) Synthetic Genes ...
After averaging: - a new row for the synthetic gene data ... during averaging) - Can have comment lines (start with #) Synthetic Genes ...
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Bioinformatics Applications of Machine Learning PowerPoint PPT Presentation
Bioinformatics Applications of Machine Learning - Some bioinformatics applications of the machine learning methods covered in the ... Smith-Waterman local alignment (includes only best-matching high-scoring regions) ...
Some bioinformatics applications of the machine learning methods covered in the ... Smith-Waterman local alignment (includes only best-matching high-scoring regions) ...
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MDMS-A Web Tool to Manage PowerPoint PPT Presentation
MDMS-A Web Tool to Manage - MDMS-A Web Tool to Manage & Analyze Gene Expression Microarray Data. Sachin Mathur ... Analysis of Early Lung Development dataset using MDMS. MDMS Demo ...
MDMS-A Web Tool to Manage & Analyze Gene Expression Microarray Data. Sachin Mathur ... Analysis of Early Lung Development dataset using MDMS. MDMS Demo ...
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Vorlesung 2 PowerPoint PPT Presentation
Vorlesung 2 - Analyse: Clustering; Class Discovery; Klassifikation; ... Twilight. SAM: Significance Analysis for Microarrays. More Scores: Wilcoxon Score (robust) ...
Analyse: Clustering; Class Discovery; Klassifikation; ... Twilight. SAM: Significance Analysis for Microarrays. More Scores: Wilcoxon Score (robust) ...
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Genomic Analysis of Prostate Cancer Cells PowerPoint PPT Presentation
Genomic Analysis of Prostate Cancer Cells - Kyle Furge, Ph.D., Van Andel Institute. Computational Biology ... Sridhar, Paul Norton from VAI, Kyle Furge from VAI, Prof. Priscilla Kimboko from ...
Kyle Furge, Ph.D., Van Andel Institute. Computational Biology ... Sridhar, Paul Norton from VAI, Kyle Furge from VAI, Prof. Priscilla Kimboko from ...
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Estimating parameters in a statistical model source"http:eh3'uc'eduteachingcfg2006RNickelLinearModel PowerPoint PPT Presentation
Estimating parameters in a statistical model source"http:eh3'uc'eduteachingcfg2006RNickelLinearModel - source('http://eh3.uc.edu/teaching/cfg/2006/R/NickelLinearModels.R' ... [1] 'contr.treatment' attr(,'contrasts')$dye [1] 'contr.treatment' attr(,'contrasts')$trt ...
source('http://eh3.uc.edu/teaching/cfg/2006/R/NickelLinearModels.R' ... [1] 'contr.treatment' attr(,'contrasts')$dye [1] 'contr.treatment' attr(,'contrasts')$trt ...
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Significance Testing of Microarray Data PowerPoint PPT Presentation
Significance Testing of Microarray Data - Permute group labels among samples. redo tests with pseudo-groups ... Permuted t -scores for many genes may be lower than from random samples from the ...
Permute group labels among samples. redo tests with pseudo-groups ... Permuted t -scores for many genes may be lower than from random samples from the ...
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ABSTRACT PowerPoint PPT Presentation
ABSTRACT - A critical event in the progression of prostate ... Josh Levy1, Toby Segaran1, Justin Sun1, David Kightley1, Bill Ladd1, Jacques Pappo1, and Keith Elliston1 ...
A critical event in the progression of prostate ... Josh Levy1, Toby Segaran1, Justin Sun1, David Kightley1, Bill Ladd1, Jacques Pappo1, and Keith Elliston1 ...
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Steilkurs in praktischer MikroarrayAnalyse PowerPoint PPT Presentation
Steilkurs in praktischer MikroarrayAnalyse - Two or more types of samples (e.g. treated cell lines, biopsies) ... R. Simon, M. D. Radmacher and K. Dobbin (2002). Design of studies using DNA microarrays. ...
Two or more types of samples (e.g. treated cell lines, biopsies) ... R. Simon, M. D. Radmacher and K. Dobbin (2002). Design of studies using DNA microarrays. ...
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