Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies - PowerPoint PPT Presentation

Jan 09, 2023 •198 likes •330 views

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics
JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics
Science! Mark Voorhies Practical Bioinformatics
Example Pipeline: Overview Mark Voorhies Practical Bioinformatics
Example Pipeline: Details Mark Voorhies Practical Bioinformatics
GSE88801 Pipelines Mark Voorhies Practical Bioinformatics
Linear Least Squares Mark Voorhies Practical Bioinformatics
Linear Least Squares b i = y i σ i Mark Voorhies Practical Bioinformatics
Linear Least Squares A ij = f j ( x i ) σ i Mark Voorhies Practical Bioinformatics
Linear Least Squares χ 2 = | A · a − b | 2 Mark Voorhies Practical Bioinformatics
Linear Least Squares M � U i · b � � a = V i s i i Mark Voorhies Practical Bioinformatics
Multiple Hypothesis Testing http://xkcd.com/882/ Mark Voorhies Practical Bioinformatics
Homework live Explore today’s limma results for the uninfected | J 77 , 24 h comparison (choose two or more) : 1 Extract the gene names from limma1.J774.Live.24-J774.uninfected.24.t0.csv and paste them into the selection window in JavaTreeView. 2 Filter yesterday’s heatmap to create a new CDT file for just these differential genes. 3 Redo our PCA and clustering protocol for just these differential genes. 4 Find the corresponding set of differential genes from the “J774 Live vs Uninfected” tab of S2 of the paper. Use python sets to find differential genes common to the two analysis pipelines. 5 Repeat the above for other interesting comparisons. Mark Voorhies Practical Bioinformatics

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