How to create a project?

To create a project, you first need to transfer the data files to the Flow server, and then import the files into your project using the import data wizard, here is the video and more information

Why do I get "?" for FDR p-values in my Deseq2 result?

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

Click here for troubleshooting other differential analysis models and "?" results

What is the difference between FDR and FDR step up?

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 the difference between GSEA and Gene Set Enrichment?

In Parte 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.

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.

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 transgenes to my reference files? 

How do I add and use my own lists?

Click your avatar in the top right corner of the Partek Flow interface, choose Settings in the menu, and select Lists from the left panel of the Components section. For more information please click here. We do provide hosted lists (from publications) for different cell types or conditions which can also be used in your analysis. Lists can also be generated from 

Can I build and use pipelines for my analysis?

Can I label the volcano plot with gene names?

How can I free up space on my server?

Can I export data from the result nodes?