Table of Contents


Online example

Goal

Detect transcriptomic markers in a set of GEO studies with the same experimental design using meta-analysis techniques.

Work plan

  1. From a browser, we access to the tool ImaGEO.
  2. Step 1. Select input: “Load examples” and two studies will be uploaded (GSE4588 & GSE10325). To start, we keep parameters by default, and submit!
  3. Step 2. Assign samples to each group: the previous selection is ok for this first time. Click “Next”.
  4. After few minutes we will have a detailed report to understand this approach.
  1. Summary / Datasets info. What do you think about the number of samples for each group? Are balanced?
  2. Interstudy Quality Control.
    • Datasets Boxplots. What is the rank for expression values?
    • Missing values. Is there a big percentage of missing values for each study?
  3. Results.
    • Differentially expressed genes summary. Are there big differences when comparing significant results for each study vs. combined studies at the same time?
    • Meta-analysis results. Could you explain the meaning of these indicators: fdr_pval, pval, zval?
    • Heatmaps. Explain a bit these graphical representations in the context of your analysis.
    • R code. We would like to repeat the process from the R code given by ImaGEO.