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FDR is the expected proportion of false discoveries among all discoveries. FDR Step-up is a particular method to keep FDR under a given level, alpha, that was proposed in this paper. In Partek Flow, if one calls all of the features with p-values 0.02 or less, the FDR is less or equal to 0.41.

What is

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

What is fold change?

In Partek Flow, fold change is in linear scale (even the input data is in log scale). It is converted from ratio, which is the LSmean of group one divided by LSmean of group two in your comparison. When ratio is greater than 1, fold change is identical to ratio; when ratio is less than 1, fold change is -1/ratio. There is no fold change value between -1 to 1. When ratio/fold change is 1, it means no change between the two groups.

Can I label the volcano plot with gene names?

Biological Interpretation FAQs

What is the difference between GSEA and Gene Set Enrichment?

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

How do I classify the cells?

How do I add the correct reference files if I am not studying human or mouse?

How can I add transgenes to my reference files? 

Can I label the volcano plot with gene names?