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.

Can I change my user avatar? 

Yes, navigate to My profile by clicking your avatar at the top right corner of the home screen, select Settings,  and click the Change image button.

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?

Yes, click on the link "Import a pipeline" on the bottom of the “Analyses” tab dashboard. This will help you import either our hosted pipelines or your own saved pipeline which can be found under Settings -> Components -> Pipelines. Click here for steps to save and run a pipeline. For more information related to navigating pipelines click here. 

My server is full, how do I make more space?

We recommend cleaning up projects as well as removing library files that you do not need, then removing the orphaned files. You can also export analyzed projects and save them on an external machine and when you need them again you can easily import them to the server. Please see this information for more details related to: Project management, Removing library files, and Orphaned files. Right click on the data node to delete files from projects that are not needed (e.g, fastqs from project pipelines that are analyzed).

Can I export data from the result nodes?

Yes, left click to select the data node you want to export. In the bottom of the task menu there will be an option to "Download data". 

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? 

How do I classify the cells?

Classification in Partek Flow can be performed manually or with automatic cell classification which is explained in more detail here. Users often want to classify cells by gene expression threshold(s), for details on classification by marker expression click here. Automatic classification needs to be performed on a non-normalized single cell data node; once complete, publish cell attributes to project then use this classification in visualizations and tasks. You may choose to perform Graph-based clustering and K-means clustering to help identify biomarkers that can then be used to identify the clusters and we also provide hosted lists for different cell types. 

Can I visualize fold change values on a heatmap without using a z-score?

Yes, the default settings can be modified by clicking "Configure" in the Advanced settings during task set-up, then change the "feature scaling" option to "none" to plot the values without scaling. For more information related to to the heatmap click here. 

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.