Import Expression Data

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Import Expression Data into Array Studio

Overview

Array Studio can import expression data, such as RNA-seq FPKM/TPM/count data, and expression Microarray data, with only a few clicks. These data will be saved as an -Omic Data object in your project. You can attach annotation and design metadata during import, or after you have created your -Omic data object.

To import expression data, click Add Data | Add Omic Data | Add Expression Data:

AddExpressionData Menu.png

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Input Data Requirements

Array Studio can import expression data from diverse source files, including tab- and comma-delimited files, Excel spreadsheets, and platform-specific file formats.

Step 1: Specify Input Data Format

AddExpressionData SpecifyExpressionDataSource.png

For details on importing different expression files as -Omic data, please visit the relevant page:

Step 2: Preview Columns (delimited files)

AddExpressionData PreviewColumns.png

If importing data from a delimited file, such as a table, any columns that contain descriptions of the data (i.e. not measurement values) should be indicated.

The only exception is the first column, which should contain sample or variable IDs, depending on whether the data are one sample per row or one variable per row, respectively

You can indicate columns by selecting individual column titles in the list (hold ctrl to select multiple items, or shift to select a range).

You can also "select by pattern", for example if descriptive columns have "desc_" as a prefix. You can also invert the selection, or clear all selections.

If you do not wish to import the metadata in the table, select descriptive columns, then check "Exclude descriptive columns".

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Step 3: Attach Design MetaData table

After importing the expression data, you can attach a design file.

AddExpressionData image014.jpg

Clicking "Yes" allows user to choose table source, while clicking "No" will proceed to next step. If user chooses not to attach a design table at this moment, they can attach one at a later stage by right clicking "Design" and choosing "Import" under Omic Data section.

Choose the right input format from the Specify Table Source window and click "OK" to continue.

AddExpressionData SpecifyDesignTableSource.png

Specify the location of the Design table file.

AddExpressionData image016.jpg

Selecting "OK" will then proceed with the data parsing and creation of the Design table.

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Step 4: Attach Annotation MetaData table

For some types of data, Array Studio can detect the annotation source when importing data, and add the annotation automatically. If the annotation files do not exist or Array Studio cannot detect annotation source according to array type or experiment platform, the user will be directed to the Attaching Annotation window.

AddExpressionData image018.jpg

Clicking "Yes" allows user to choose annotation table source. If user chooses not to attach a design table at this moment, they can attach one at a later stage by right clicking "Annotation" and choosing "Import" under Omic Data section.

Choose the right input format from the Specify Table Source window and click "OK" to continue.

AddExpressionData SpecifyAnnotationTableSource.png

Specify the location of the annotation table file and click "Open" to finish attaching the annotation.

If you select "Online annotation file", you can select among many annotation files that are provided by OmicSoft, covering popular array platforms and gene annotations:

AddExpressionData SelectOnlineAnnotation.png

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Example Results

After importing your expression data, you will find a new -Omic data object in the Solution Explorer:

AddExpressionData FinalObject.png

If you attached Annotation or Design MetaData tables during importing, they will also be displayed here. If you would like to attach or append metadata later, you can right-click the Annotation or Design folder in your object, and select Import.

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