how to find different expressed genes in GEO2R and do I have to apply a process to the results I get from GEO2R

Question

[eckmk]

Hi everyone, I am working with gene expression analysis and I just started working in this area. I have downloaded three datasets from GEO database and analyze with GEO2R. I downloaded the data results and want to draw venn diagram. but I could not get overlap between different sets of differentially expressed genes. where am i doing wrong Do I have to apply a process to the results I get from GEO2R? how should i apply?

Answer 1

[Kevin Blighe]

If there are no statistically signficantly differentially expressed genes that overlap across any 2 studies, then this may be the genuine result.

Some things at which to look:

• are the gene identifiers the same? if you are using gene symbols, then it may be best to convert these to a standardised format, like Ensembl or Entrez gene IDs, and then gauge overlap
• check your cut-offs for statistical significance
• do the 3 studies have the same experimental design?
• are the same conditions / groups being compared in each study?
• are there outliers in any of the studies that could affect the statistical inferences that are being made on the data?

Thank you.

Kevin

[eckmk]

Thank you for your advice Kevin. I will try again considering your suggestions.