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University of Wisconsin–Madison

Bioinformatics Resource Center

The UW Biotechnology Center is following University guidelines regarding COVID-19.

We understand how this disruption of service has impacted your research and we are continuing essential projects.

Advanced mRNAseq Differential Gene Expression Workshop

2020 Dates: TBA

Prerequisites:
- Linux Essentials workshop (or proficiency in bash shell commands)
- mRNA-Seq Workshop (or proficiency assertion) 
- Prior experience with software R; (acquaintance with Rstudio useful.)

Location: Genetics/Biotech Center
425 Henry Mall Madison, WI 53706 

LIMITED to 5 participants - (2 minimum)

REGISTER: use Google Calendar link to register on chosen date

Description

There will be a series of advanced workshops focusing on various aspects. This is the first of the series.

This workshop is meant to further explore differential gene expression analysis (DEG) in more depth (particularly on statistical methods and normalization) and focus on visualsing and interpreting DEG results.

We will review methods pertinent to:
- data distribution,
- raw data filtering,
- read-counts interpretation and normalization caveats with F/RPKM, 
- multidimensional scaling (MDS) and PCA,
- statistical analysis: hypothesis testing, multiple testing, dispersion, 

In the process we will make heavy use of the software R and specific packages within: DESeq2, edgeR, and possibly more.

The R package ggplot2 provides fantastic graphical presentations and will be used during the examples.

This is an all day workshop with emphasis on hands-on exercises.

Participants are expected to have a minimum basic knowledge of the Linux environment (bash shell) and a basic understanding of statistical methods (in particular FDR and multiple correction.)

Prior experience with R is necessary and some experience with RStudio would be an asset.

Prerequisites:

1. Must be comfortable with the Linux command line (bash shell). (If you have registered for the Linux Basic for NGS Data Analysis  you are considered to meet the prerequisite.)
2.Previous attendance of the mRNA-seq workshop or proof of linux-based method proficiency required.
3. Prior experience with R

* There is a minimal set of software that should be installed on laptops BEFORE attending the workshop. Instructions will be provided to attendees prior to the workshop and can be found within the PDF document: GETTING PREPARED FOR CLASS  

Fee: $350/ seat

Instructors:
Jean-Yves Sgro,  Ph.D., Biotechnology Center - jsgro@wisc.edu

*No-show Policy*
All cancellations needs to be notified 72 hours in advance.