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How we can use DEG data for GSEA analysis

Hello greetings to all, Here, I have the same questions? The excell of my DEG data have different values such as read count, TPM, FPKM, N of individuals samples in a certain group. Thus which values we will use to analyze the GSEA? Thank you,

gsea
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written by yeshiwork2000 • yeshiwork2000

Nice tutorial here, core GSEA now supports normalized counts as mentioned by @rodolfo.

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written by badribio badribio

1 answer

Hi!

According to the Broad institute guidelines you should run GSEA using a non-pre-ranked method. For this purpose, if you are analyzing your data with DESeq2 or edgeR packages you must retrieve and use normalized counts using the median of ratios or TMM methods, respectively. Both methods make comparable dataset among samples. Avoid using raw counts, TPM or FPKM because the last normalization methods are not aware of library composition.

Best regards!

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written by rodolfo.peacewalker • rodolfo.peacewalker

Thank you for your response brother, can we have a conversation via email, yeshiwork2000@gmail.com workneh.korma@aau.edu.et Thank you,

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written by yeshiwork2000 • yeshiwork2000

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