ncibtep@nih.gov

Bioinformatics Training and Education Program

Analysis with Partek Genomics Suite: mRNA, miRNA, Methylation and More

Analysis with Partek Genomics Suite: mRNA, miRNA, Methylation and More

 When: Dec. 13th, 2017 9:30 am - 4:00 pm

To Know

Where:
NIH Bldg 10, FAES Room 4 (B1C205)
Organizer:
BTEP
Class Files:
Files
This class has ended.
Video Archive *Class recordings may take ~48 hours to become available.

About this Class

PLEASE NOTE: This workshop is a BYOC (Bring Your Own LapTop Computer) class, and requires installation of Partek Genomics Suite on your laptop ahead of the workshop. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer, please indicate such in the Comment section on the registration form. WORKSHOP AGENDA 9:30 am – 12:30 pm         Gene Expression Analysis with Partek Genomics Suite This training session will include a guided analysis of an Affymetrix gene expression data set to showcase and familiarize users with the Gene Expression analysis workflow covering the topics listed below.
  • Importing data – Affymetrix CEL files
  • Exploratory data analysis – Principal Component Analysis (PCA)
  • Detecting differential expression (ANOVA) – two factor analysis
  • Gene list creation (Venn diagram creation and list overlap)
  • Visualization (PCA, histogram, box plot, dot plot, volcano plot, heatmap etc.)
  • Biological interpretation – through use of Gene Ontology and KEGG
  Additional advanced topics will include:
  • Integration with other data – combining gene and miRNA expression data
  • Batch effect removal
  • Survival analysis
  12:30 – 1:30 pm LUNCH BREAK   1:30 – 3:00 pm           Advanced Modules This session will provide a hands on training for analyzing Illumina methylation microarrays, familiarizing users to the topics listed below.
  • Importing data – Illumina .idat files
  • Data normalization – converting data to M-values
  • Exploratory data analysis – Principal Component Analysis (PCA)
  • Detecting differential methylation (ANOVA)
  • Annotating markers by gene section
  • Visualization (PCA, histogram, box plot, dot plot, volcano plot, heatmap etc.)
This session will also provide the opportunity to learn how to import and process data matrices in text file format (from RNA-seq or protein data, as an example) for the purpose of generating visualizations.   3:00 – 4:00 pm         Bring Your Own Data/Independent Analysis of GEO Data
  •   Bring your own data for analysis help.
-OR-
  •  Attendees will be presented with the task of obtaining a data set from the NCBI Gene Expression Omnibus (GEO) and running an independent analysis of the data to attempt to replicate the findings of the publication.  They will be given a list of analysis goals and will have the opportunity to ask for help from the instructor as they work through this analysis.
The two PDF files below (Course Material 1 and 2) document the workflows that will be followed, and also contains links to the example datasets that attendees will use during the workshop. Kindly download the data if you plan to attend.
 

Files

  • NCI_Partek_MicroarrayMethylation_Workshop.pdf: |
  • NCI_Partek_MicroarrayExpression_Workshop.pdf: |