Course Live Advanced Dr. Omics Edu

Transcriptomic Profiling Masterclass: From GEO Raw CEL Files to Cytoscape Networks

A hands-on transcriptomics masterclass covering GEO microarray CEL files, preprocessing, differential expression, functional analysis, and Cytoscape-based gene network visualization.

  • 5.0/5
  • English
  • Updated Oct 2026
INR

₹45000

₹60000 25% off
USD

$600

$700 14% off

Indian learners pay in INR; international learners are billed in USD.

Enroll for International Students

Paying from outside India? Use this link to complete your payment.

Make an Enquiry
Transcriptomic Profiling Masterclass: From GEO Raw CEL Files to Cytoscape Networks

About this course

The Transcriptomic Profiling Masterclass: From GEO Raw CEL Files to Cytoscape Networks at Dr. Omics Edu is a live, mentor-led online course in microbiome, metagenomics and transcriptomics. It takes raw GEO CEL files all the way to interpretable gene networks in Cytoscape. You learn on real biological data and finish with an omics dataset analysed from raw data to biological interpretation that you can show to an employer, a guide or an admissions panel.
In this course you move through finding and downloading datasets from ncbi geo, reading raw cel files and quality control and normalisation and differential expression, then apply them in a hands-on project. The course runs live online across 1 module, so you can ask your mentor questions as you work. It is an advanced-level course, best suited to learners who already know the fundamentals.

What you will learn

Understand the fundamentals of transcriptomic and microarray data analysis.
Retrieve and work with raw CEL files from the GEO database.
Perform quality assessment and preprocessing of microarray data.
Understand background correction, normalization, and expression summarization.
Identify differentially expressed genes between experimental conditions.
Generate and interpret common transcriptomic visualizations.
Perform functional enrichment and pathway analysis.
Construct and analyze gene interaction networks.
Import and visualize biological networks using Cytoscape.
Interpret transcriptomic and network-analysis results in a biological context.
Microbiome data analyst, metagenomics analyst, transcriptomics analyst, research associate.

Skills you will gain

R Bioconductor limma GEO STRING Cytoscape
Certification

Available

Issued by Dr. Omics Edu

Course curriculum

1 module

  • Day 1 – Introduction to microarray technology and platform types (Affymetrix).
  • Day 2 – Mining and downloading datasets from GEO (Gene Expression Omnibus).
  • Day 3 – Understanding raw microarray data structures (CEL files) and experimental design considerations.
  • Day 4 – Quality assessment using NUSE (Normalized Unscaled Standard Error) plots.
  • Day 5 – Quality assessment using RLE (Relative Log Expression) plots and identifying outlier arrays.
  • Day 6 – RMA normalization fundamentals using oligo/affy packages.
  • Day 7 – Differential expression analysis setup with limma (design matrix, contrasts).
  • Day 8 – Running limma analysis and interpreting moderated t-statistics/eBayes results.
  • Day 9 – Probe annotation and ID mapping (probe-to-gene symbol conversion).
  • Day 10 – Cross-platform validation: comparing microarray results with RNA-Seq data.
  • Day 11 – Advanced visualization: volcano plots and MA plots for DE results.
  • Day 12 – Advanced visualization: ComplexHeatmap for expression patterns and sample annotations.
  • Day 13 – Functional enrichment analysis with clusterProfiler (ORA) and GSEA methodology.
  • Day 14 – Pathway and network biology using STRING and Cytoscape for interpreting gene networks.
  • Day 15 – Doubt session

What you need to start

  • Basic understanding of molecular biology, genetics, or gene expression.
  • Basic knowledge of bioinformatics concepts is recommended.
  • Familiarity with Linux or R is helpful but not mandatory.
  • Basic computer skills.
  • No prior experience with GEO or Cytoscape is required.

Who this course is for

  • B.Sc, M.Sc, B.Tech, M.Tech and PhD students in microbiology, biotechnology, genetics or life sciences.
INR

₹45000

₹60000 25% off
USD

$600

$700 14% off

Indian learners pay in INR; international learners are billed in USD.

Enroll for International Students

Paying from outside India? Use this link to complete your payment.

Make an Enquiry
Active batch
Open for enrolment
Cancer Gene Expression Profiling (Microarray Workflow)
  • Starts 19 Oct 2026
  • Ends 06 Nov 2026
  • Timing 7:00 PM – 8:00 PM
  • Days Mon, Tue, Wed, Thu, Fri
  • Platform MS Teams
This course includes
  • Format Live
  • Level Advanced
  • Language English
  • Modules 1
  • Certificate Yes
  • Provider Dr. Omics Edu
  • Live
  • instructor-led interactive sessions.
  • Hands-on analysis using representative GEO microarray datasets.
  • Practical experience with raw CEL files and transcriptomic workflows.
  • Step-by-step guidance through preprocessing and differential expression analysis.
  • Functional enrichment and pathway-analysis exercises.
  • Hands-on STRING and Cytoscape network analysis.
  • Supporting datasets and learning resources.
  • Course materials for reference and practice.
  • Certificate of participation/completion as applicable.
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