## Importing Illumina data

You have two alternative ways to import Illumina data. Your choice of import method affects the choice of the subsequent normalization method as described below:

1. Import the file directly
   When you get the "Import files" dialog window, change the Action to "Import directly" and click "OK". Note that your all your samples need to be in the same, intact BeadStudio/GenomeStudio file. In addition to the identifier column (preferably ProbeID) the file needs to have the columns AVG, BEAD_STDERR, Avg_NBEADS and DetectionPval. When you have imported your data this way, you have to use the normalization Illumina - lumi pipeline.
2. Use import tool
   When you get the "Import files" dialog window, leave the Action to "Use Import tool" and click "OK". This gives full control on what samples from the BeadSummaryData files you would like to import and which samples you would like to normalize together. Below is a short description on how to use the Import tool for Illumina data. For more information, please see the Import tool manual. Note that when you have imported your data this way, you have to use the normalization tool Illumina.

When you have selected file(s) to import, the "Import files" dialog opens. Select the Action "Use Import tool" for all your files.

Clicking "OK" opens the first window of the Import tool. Define the title row by clicking on the "Mark title row" -button on the top, and click the row you want to mark as a title row. If your data was created with BeadStudio version 1 or 2, your file also contains a header which needs to be marked (click on the Mark header -button on the top, and paint the rows you want to mark as a header).

Next you need to select the columns you would like to import to Chipster. The exact column names in the original data file vary depending on which BeadStudio/GenomeStudio version (1-3) was used for creating it. However, the columns with "AVG" always contain the expression values and should hence be labeled as "sample" in the Import tool.

- If your data file was created with BeadStudio version 1 or 2, label the TargetID column as "identifier".
- If your data was created with BeadStudio version 3 or later, label the ProbeID column as an identifier instead. Note that for some versions one needs to use the PROBE_ID column for HT-12 arrays.

To define the columns, select the meaning by clicking on the button on the top of the page, and then click on one of the columns (not the greyed header).

To conclude the import, click on the Finish-button. After the data has been imported, it is displayed as several files (as many files as sample columns were selected) under Datasets and in the Workflow view. Now the data has been successfully imported, and you should normalize it. You can also run some quality control checks after the normalization.