I have gene expression data from different conditions from different studies. Instead of using the actual TPM values for Pearson Correlation coefficient (PCC) calculation, I have decided to use Fold change values from different studies to eliminate biases from different studies. My question is whether using these raw fold change values for identifying co-expressed genes is a correct way to do it or should perform quantile normalization on these fold change values before using them for PCC calculation? (Note: Distribution of fold change values in different studies is quite different)
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Last edited by Jayesh; 12-19-2019, 10:30 AM.
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