The Partek^® Flow^® Data Tab is where users can add samples, import data, and assign sample attributes. This is also where users can modify the location of the project output folder.

Table of Contents

Adding samples

For a new project, where no samples have yet been added, the Data tab will automatically prompt you to add samples (Figure 1). To add samples to the project, click Import data. Four options will be displayed.

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Automatically create samples from files

This method adds samples by creating them simultaneously as the data gets imported into a project. The sample names are assigned automatically based on filenames.

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Create a new blank sample

Samples can be added one at a time by selecting the Create a new blank sample option (Figure 6). In the following dialog box, type a sample name and click Create. This process creates a sample entry in the sample management table but there is no associated file with it, hence it is a "blank sample."

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Adding Files to an existing project

Additional samples can be added to any existing project simply by opening the project, going to the Data tab, and clicking the Import data button (Figure 7). Three options to add samples will be revealed.

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Importing feature counts

Alternatively, if you have a matrix of data, such as raw read count data in text format, select Import feature counts. This will bring up the Input options page (Figure 8).

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Project output directory

The project output directory is the folder within the Partek Flow server where all output files produced during analysis will be stored.

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The user has the option of specifying an existing folder or creating a new one as the project output directory. To do so, click the  icon next to the directory and specify or create a new folder in the dialog box.

Sample Annotation

After samples have been added in the project, additional information about the samples can be added. Information such as disease type, age, treatment, or sex can be annotated to the data by assigning the Attributes for each sample. 
Certain tasks in Partek Flow, such as Gene-Specific Analysis, require that samples be assigned attributes in order to do statistical comparisons between groups or samples. As attributes are added to the project, additional columns in the sample management table will be created.

Sample attributes

Attributes can be managed or created within a project. Under the Data tab, click the button to open the Manage attributes page (Figure 10).

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To prepare for later data analysis using statistical tools, attributes can either be categorical or numeric (i.e., continuous).

Adding a categorical attribute

For categorical attributes, there are two levels of visibility. Project-specific categorical attributes are visible only within the current project. System-wide categorical attributes are visible across all the projects within the Partek Flow server, and are useful for maintaining uniformity of terms. Importing samples in a new project will retain the system-wide attributes, but not the project-specific attributes.

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Adding a numeric attribute

To add a numeric attribute in the Manage attributes page, click the Add new attribute. In the dialog box (Figure 13), type a Name for the attribute, select the Numeric radio button next to Attribute type, and then click the Add button. Some optional parameters for numeric attributes include the Minimum value, Maximum value, and Units. When done, click Add to return to the Manage attributes page. Repeat the process add more numeric attributes. When done, click Back to sample management table.

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Adding a system-wide attribute

Since system-wide attributes do not have to be created by the current user, they only need to be added to the sample management table in a project.

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Assigning categories or values to attributes

After adding all the desired attributes to a project, the sample management table will show a new column for each attribute (Figure 15). The columns will initially as "N/A", as the samples have not yet been categorized or assigned a value. To edit the table, click  . Assign the sample attributes by using a drop down for categorical attributes (controlled vocabulary) or typing with a keyboard for numeric attributes.

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• If the previous attributes have the same header and type (both are either categorical or numeric), the values are overwritten.
• If there are different/additional headers on the "second round" of assignment, these new attributes will be appended to the table.
• For numeric attributes, a "blank" value will not override a previous value. 

Deleting or Renaming samples within a Project

In the Data tab, each sample can be renamed or deleted from the project by clicking the gear icon next to the sample name. The gear icon is readily visible upon mouse over (Figure 18). Deleting a sample from a project does not delete the associated files, which will remain on the disk.

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You can download your completed Sample management table by clicking the Download link at the lower corner of the table. This will export a tab-delimited text file with contents of the table.