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Customarily, when two conditions are listed A and B, and a foldchange is mentioned, it means the ratio of B/A, second condition relative to the first condition That is the most common convention. In this case, bored vs excited, a fold change of 4 would mean that ratio excited/bored = 4 |
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Hello,
I am practicing RNA-seq analysis through the RNA-seq by example handbook and I have a question regarding fold change. Since the design.csv contains sample "bored 1,2,3 and excited 1,2,3" and condition "bored, excited". When Deseq2 was performed, gene "AAA-750000-UP-4 has log2foldchange of 2.2. Does this mean condition "bored" was upregulated 2.2 times compared to the condition "excited" or is it reverse? Could you please clarify the order of the foldchange?
Thank you,
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