Why are all adjusted p-values are the same in the DESeq2 result?

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The "padj" values in DESeq2 represent the adjusted p-values for each gene after controlling for multiple testing. These adjusted p-values are calculated using a method called the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR) at a specified level.

If all the padj values are the same for all genes, it suggests that there may be a problem with the input data or the DESeq2 analysis. One possibility is that the input data may not have sufficient variability, such as when all samples are very similar or there is very little differential expression between groups. Another possibility is that there may be an issue with the analysis parameters, such as setting an incorrect normalization method or not specifying the correct experimental design.

To investigate this issue further, it is important to review the input data and the DESeq2 analysis parameters to identify any potential sources of error. It may also be helpful to consult with a bioinformatician or seek help from the DESeq2 user community to troubleshoot the issue.

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