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Exercise

Normalizing counts with DESeq2

We have created the DESeq2 object and now wish to perform quality control on our samples. Therefore, we need to generate the normalized counts (normalized for library size, which is the total number of gene counts per sample, while accounting for library composition). To obtain the normalized counts, use the DESeq2 object and generate the normalized counts matrix.

Instructions

100 XP

  • Estimate the size factors for the smoc2 count data using the estimateSizeFactors() function and save back to the dds_smoc2 object

  • Extract the normalized count values from dds_smoc2 and save as smoc2_normalized_counts using the counts() function.