General FAQs

How to create a project?

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

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 and lists can also be generated from result tables. 

Can I build and use pipelines for my analysis?

How can I free up space on my server?

Can I export data from the result nodes?

Statistics FAQs

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 features to exclude low expression features before Deseq2, or in the Deseq2 advanced options, choose apply independent filtering setting. 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 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 a Volcano plot with gene names?

Yes, go to Style in the Data Viewer and make sure Gene name is selected under "Labeling". Next, go to the in plot selection tools (right side of the graphic) and use any of the selection tools to select the cells that you would like to label. You can use ctrl or shift to select multiple populations at once. For more information on the Volcano plot click here. 

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?