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I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested in determining the statistical significance of these fold changes.

What I've tried: I initially considered using limma, but I wasn't sure if it was appropriate for pre-calculated fold change values.

What I was expecting: I was hoping to obtain a list of genes with their corresponding p-values and adjusted p-values, indicating their significance. Ideally, this would help me identify genes that are significantly upregulated or downregulated in the mutant compared to the wild type.

Given that I only have the fold change values for two biological replicates (and no raw intensity or count data), what would be the best approach to achieve this? Any guidance, recommended tools, or R packages would be greatly appreciated!

Thank you in advance!

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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
    Oct 26, 2023 at 14:56

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