From Informatics

Contents 1 Functionality Enhancements and Modifications 1.1 Marker and Array Set Combination Operations 1.2 New version of caBIO 1.3 Server Side Computing 1.4 Workspace Saving Upon App Exit 1.5 Integration of Marker Annotation/caBIO Pathways Components 2 Not Yet Implemented 2.1 Support for Illumina Oligo chips 2.1.1 Data Format 2.1.2 FAQ

Functionality Enhancements and Modifications

Marker and Array Set Combination Operations

Users can create new marker and array sets by applying intersection, union and exclusion operations on multiple selected sets. For a full description of the functionality, see Mantis report #992.

New version of caBIO

The Marker Annotations component has been updated to use the new version 4.0 of the caBIO API.

Server Side Computing

Full support for server side computing has been added (Dispatcher architecture) to facilitate the execution of long running jobs. The new architecture allows submitting an analysis request in one application session and retrieving the analysis results in another.

Workspace Saving Upon App Exit

The application now queries the user if they want to save their workspace before exiting.

Integration of Marker Annotation/caBIO Pathways Components

These two components have been combined into one per the requirements specified at:

  http://wiki.c2b2.columbia.edu/mantis/view.php?id=1302

Not Yet Implemented

Support for Illumina Oligo chips

Data Format

Format specification of the Illumina chips is as follows (Illumina raw data):

Source: BeadStudio Gene Expression Module: User Guide p.110 (Illumina, Inc. 2006)

Source: BeadStudio Gene Expression Module: User Guide p.111 (Illumina, Inc. 2006)

Source: Gene Expression on Sentrix Arrays: Direct Hybridization System Manual p.103 (Illumina, Inc. 2003)

Sample raw data file from Don Swan/Alex Yemelyanov

• Media:GroupProbeProfileForCaBIG.TXT

Correponding BioConductor File (for reference and convenience)

• Media:BioConduct.XLS

FAQ

• In the BeadStudio 2 Gene Expression Module, the MIN_Signal, AVG_Signal, and MAX_Signal columns all have the same value. What is wrong?

Nothing is wrong with the data. The MIN, AVG, and MAX columns only have different values when the grouping function is used to analyze multiple 
arrays or BeadChips. If you look at the NARRAYS column, the number 1 appears. This means that only 1 array was reported as a group in this analysis; 
therefore, the MIN, AVG, and MAX values are the same.

Source: Illumina FAQ --> Software --> BeadStudio