Pathway Analysis Interpretation
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3 months ago
enh • 0

I performed a DE pairwise analysis between conditionA and conditionB using DESeq2 and proceeded to kegg pathway analysis where I get the pathways downregulated and upregulated for my conditionAvsconditionB comparison, but I'm unsure of how to interpret the results. Are the pathways upregulated in conditionA compared to conditionB or are they upregulated in conditionB compared to conditionA?

My foundations are lacking and I haven't been able to find any resources the explain how to interpret the results any help/clarifications are greatly appreciated.

analysis kegg pathway rna-seq • 390 views
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Hi!

Would you like to share with us the result from running the next command on your DESeq object? resultsNames(dds)

We can see there whether comparison was done as conditionA vs conditionB or vice versa.

Best regards!

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Hi Rodolfo, I was actually able to make sense of the returns by referencing a different post on here! the comparison was done as conditionA vs conditionB, thank you!!

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It´s alright! This is a helpful function if you are not sure about the direction of comparison. As a suggestion, when you construct your DESeq object use the relevel function to notice DESeq2 what is your reference (or control) group.