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I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data.

However, I am struggling to understand their specific purpose, differences between them and underlying theory. The information is required for a thesis with an imminent deadline

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Oct 29, 2022 at 15:11
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    $\begingroup$ Hi @noor-fatimah, your question seems quite broad and not tied to a specific problem; are you able to make your question more specific, or give some more information on what you've already found out? Have you, for example, read the user's guides for EdgeR and DESeq2? $\endgroup$
    – gringer
    Commented Oct 30, 2022 at 11:08
  • $\begingroup$ i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that $\endgroup$ Commented Nov 9, 2022 at 15:27

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I think your question has been answered very well here: https://www.biostars.org/p/284775/

If you want to go deeper perhaps you can look at this paper by Li et al. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4 where they argue that for large scale datasets (multiple conditions) both of these methods are not optimal and instead suggests using Wilcoxon rank-sum test to decrease chances of FDRs.

Best,

av

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  • $\begingroup$ i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that $\endgroup$ Commented Nov 9, 2022 at 15:29

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