IPA-Data Upload Workflow

Data Upload Workflow

Use Dataset Upload to import your dataset file into IPA.  Once uploaded, many different analysis options exist including IPA-Biomarker, IPA-Tox, IPA-Metabolomics and Core Analyses. Review the different type of analyses and see which one best fits your needs. For more information on these analyses, click here.

1.To upload a dataset file, Go to File, Upload dataset.

2. Select the dataset file from your computer and click the Open button.

3. Select a Flexible Format from the dropdown menu.

4. Select an Identifier Type from the dropdown menu. IPA supports many identifiers and symbols and will attempt to guess at the type of identifier in your dataset file. To override the selection, uncheck the option and simply select the most appropriate one. If more than one type of identifier exists in your dataset, select all appropriate ones.

5. Select the Array platform used for experiments. For more information, click here.

6. Specify the contents of each column in your dataset and review how IPA labels each column in your dataset file.

• Flexible Format. IPA will attempt to identify which column contains identifiers. To override any column assignments, simply select a different option in the dropdown menus. IPA assumes that the leftmost column contains identifiers and the remaining columns to the right contain expression values for different observations.

To override the automatic column assignments, select an option from the dropdown menus. First, group the columns by observation. If two columns are a part of one observation, select the same observation number for each column. Next, assign the expression value type for those two columns. Follow the same steps for the remaining columns.

If the dataset file contains extraneous columns of information, i.e. the columns contains notes or information not    needed for the analysis, select Ignore in the dropdown menu.

Shortcuts:

1. Ignore: Right-click a column and select Ignore.

2. Repeat Selection: Select a column(s), right-click the selected columns and select Repeat Selection. The assignments made for the selected columns will be repeated for the columns to the right of the selected ones.

3. Header Names -> Observation Name: This selection will take the name found in the column header and use it to label the observation.

4. Group In: Select more than one column, right-click the selected columns and select Group In. The selected columns will be grouped as an observation.

7. Edit Observation Names. If the dataset file is in either Ingenuity formats, then the column headers are automatically used to label the observations. Click the Edit Observations Names button to rename the observations.

8. Click the Save or Save & Create Analysis button to proceed. As part of Dataset Upload, the only option is to the save the uploaded dataset to the Project Manager. If you are creating an IPA-Biomarker, Core, IPA-Metabolomics, or IPA-Tox Analysis, clicking the Save & Create Analysis button will take you to the appropriate Create Analysis page.

9. From the Project Manager, if you double click on a dataset, the Enriched dataset will open and will display the Mapped IDs, UnMapped IDs, and All IDs.