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

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?

genes venn expressed different geo2r
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written by eckmk • eckmk

1 answer

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

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written by Kevin Blighe Kevin Blighe

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

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written by eckmk • eckmk

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