The CMSB-NBIC Rosetta Resolver server

(last updated August 29th 2011)


Preparing Illumina Data For Import Into Rosetta Resolver

Illumina patterns and scans are processed differently than other technology patterns. Successful import of Illumina data into Rosetta Resolver requires correct data export from GenomeStudio, which has replaced BeadStudio.

Before you start:

1) Check if the pattern you already exists. See www.lgtc.nl/rosetta/ for more information. If not, ask your Rosetta Resolver lab manager to prepare Illumina pattern data as described in the last part of these instructions.

2) You must also properly set up the Illumina project. Set up the Illumina project first.

To set up the Illumina project

1). Set the project name in BeadStudio to a name that is unique to existing Experiment Definition names in the Resolver system. The grouping of the samples is used to create a combine Experiment Definition where each group in BeadStudio will become a treatment group in the Experiment Definition, and the Experiment Definition takes the project name specified in BeadStudio.

2). In BeadStudio, find the project wizard window named Please choose analysis type and parameters; set the analysis type to gene expression and the normalization parameter to none.

3) Create separate chip barcodes for every sample on the BeadChip using the Chip Manager using the correct pattern. The format chip barcode number with suffix _A, etc. as used in the column headers of the spp-file works fine.

To Export Scan Data From Illumina Beadstudio or Illumina GenomeStudio

BeadStudio Version 3.0 Instructions

1. Select Analysis, and then select Create Final Report.

2. Under the Table column, select (check) Sample Probe Profile.

3. Under the Columns column, select (check) TargetID, ProbeID, the sample columns, and all subcolumn items.

Note The species column should be selected but no other annotation columns. If no species column is available, the file cannot be loaded via the AutoImporter. It must be loaded manually through the Import Manager.

4. Under the Table column, select (check) Control Probe Profile.

5. Under the Columns column, select (check) TargetID, ProbeID, and all sample data column items and subcolumn items.

6. Under the Table column, select Samples Table.

7. Under the Columns and Subcolumns column, select all items.

8. Type a file name in File Name using the extension .spp and select OK. The file is available to be loaded through the import manager or the AutoImporter.

BeadStudio Version 3.1-3.2 and GenomeStudio Version 1.1.1. Instructions

1. From the Analysis drop-down, select Reports, and then select (check) Final Report.

2. Under the Table column, select (check) Sample Probe Profile.

3. Under the Columns column, select (check) TargetID, ProbeID, the sample columns, and all subcolumn items.

Note

No other annotation columns should be selected. The only exception is the species column, which needs to be present in files loaded via the AutoImporter. Final reports loaded manually through the Import Manager do not need the species column.

4. Under the Table column, select (check) Control Probe Profile.

5. Under the Columns column, select (check) TargetID, ProbeID, and all sample data column items and subcolumn items.

6. Under the Table column, select Samples Table.

7. Under the Columns and Subcolumns column, select all items.

8. Type a file name in File Name using the extension .spp and select OK.

Note for GenomeStudio users

Column headers generated by GenomeStudio may contain a dot (e.g. 4621891204_A.AVG_Signal), which needs to be changed into a colon (e.g. 4621891204_A:AVG_Signal. This has to be done for the [Sample Probe Profile] and [Control Probe Profile] sections, using Excel, Wordpad or another texteditor. Save modified files under a new filename

The .spp file is ready to be loaded into Rosetta Resolver through the import manager or the AutoImporter.

9. In case of import problems, check the .spp file using Excel, Wordpad or another texteditor. Save modified files under a new filename

The file should have 4 parts:

[Header]
several lines
[Sample Probe Profile]
1 Column header line
1 line for each Sample Probe
[Control Probe Profile]
1 Column header line
1 line for each Control Probe
[Samples Table]
1 Column header line
1 line for each sample

Preparing Illumina Pattern Data For Import Into Rosetta Resolver (information for lab managers)

For commercially available arrays, which can be used by different groups, your lab manager has to send the pattern file to the Rosetta Resolver admin team, who will load the pattern and make it available all users. Your lab manager is only allowed to load custom patterns using descriptions starting with your institutions abbreviation (e.g. AMC_, LUMC_, UL_, VUMC_, etc.)

To Export Pattern Data From Illumina Beadstudio

BeadStudio Version 3.0 Instructions

1. Select Analysis, and then select Create Final Report

2. Under the Table column, select (check) Sample Probe Profile.

3. Under the Columns column, select (check) TargetID, ProbeID, and all annotation items. Do not select any items representing sample data.

4. Under the Table column, select (check) Control Probe Profile.

5. Under the Columns column, select (check) TargetID and ProbeID.

6. Type a file name in File Name and select OK. The file can now be loaded into Rosetta Resolver through the import manager.

BeadStudio Version 3.1-3.2 and GenomeStudio Version 1.1.1. Instructions

1. From the Analysis drop-down, select Reports, and then select (check) Final Report.

2. Under the Table column, select (check) Sample Probe Profile.

3. Under the Columns column, select (check) TargetID, ProbeID, and all annotation items. Do not select any items representing sample data.

4. Under the Table column, select (check) Control Probe Profile.

5. Under the Columns column, select (check) TargetID and ProbeID.

6. Type a file name in File Name and select OK. The file can now be loaded through the import manager.