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Because different samples have different total numbers of total reads, it would be misleading to calculate differential expression by comparing read count numbers for genes across samples without normalizationnormalizing for the total number of reads. 

• Select the Gene Click the Filtered counts data node
• Select Click Normalization and scaling from in the task menu
• Select Click Normalize counts from the Normalization and scaling section of the task menu (Figure 1)
  
  

The Read count normalization menu will open (Figure 2).

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Normalization can be performed by sample or by feature. By sample is selected by default; this is appropriate for the tutorial data set. 

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Total Count normalizes read counts for each gene by the total count of the sample. This accounts for differences in total read counts between samples. 

Add 0.0001 adds 0.0001 to the normalized read count of every gene. This prevents the read count data from having any 0 values. Values of 0 would prevent the gene specific analysis algorithm we will use for differential expression analysis from performing the necessary log transformation. 

• Select Click Finish to perform normalization

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