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When a feature (gene) has low expression, it will be filtered by automatic independent filtering. To avoid this, you can either perform filter feature features to exclude low expression features before Deseq2, or in Deseq2 advanced option configuration, change Appy options,  apply an independent filtering setting to No. Details about independent filtering can be found at Deseq2 documentation. 

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What is the difference between GSEA and Gene Set Enrichment?

In Parte Partek Flow, GSEA should perform on a sample/cell and feature matrix data node, e.g. normalization count data. It is to detect a gene set/a pathway is significantly different between two groups. Gene set enrichment should be performed on a filtered gene list, it is to identify overrepresented gene set/pathway based the filtered gene list using Fisher's exact test. The input data is a filtered list of gene name.

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