How to perform differential expression analysis of metabric data obtained from METABRIC?
I have downloaded metabric data from cbioportal. The folder contains files as follows:
1. data_expression_median.txt
2. data_mRNA_median_all_sample_Zscores.txt
3. data_mRNA_median_Zscores.txt
Which file should I consider for differential expression (DE) analysis. Since Deseq2 and EdgeR requires input as raw_counts, the above files are not useful to perform DE analysis.
Please suggest me the possible methods to perform DE analysis on this dataset.
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Nitin Narwade
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DareDevil
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These are all the normalized counts and you can only run DESeq/EdgeR on the raw count.
Usually, I perform tests like Wilcoxon rank-sum test and consider median expression to calculate the fold change between two groups. It might not be a good way but I apply a really stringent p-value and fold change cut-off to consider the differentially regulated genes.