Version 2.6 (R2007a+) Bioinformatics Toolbox™ Software Release Notes

Version 2.6 (R2007a+) Bioinformatics Toolbox Software

This table summarizes what's new in Version 2.6 (Release 2007a+):

New and updated functions in this version include:

• Data Formats and Databases Functions

• Microarray File Formats Functions

• Microarray Utility Functions

• Microarray Normalization and Filtering Functions

• Mass Spectrometry Functions

• Demos for Mass Spectrometry Functions

Data Formats and Databases Functions

The following functions are updated:

• affyread — Read microarray data from Affymetrix GeneChip file. Updated to read Affymetrix files from expression, genotyping, or resequencing assays on all platforms, except Solaris™.

• celintensityread — Read probe intensities from Affymetrix CEL files. Updated to read Affymetrix CEL and CDF files from expression or genotyping assays on all platforms, except Solaris.

• mzxmlread — Read mzXML file into MATLAB as structure. Updated to read mzXML files that conform to the mzXML 2.1 specification or earlier specifications.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.6, the structure returned by affyread when reading a CHP file from an expression assay no longer contains a ProbePairs field. The ProbePairs field still exists in the structure returned by affyread when reading a CDF file.

Microarray File Formats Functions

The following functions are updated:

• affyread — Read microarray data from Affymetrix GeneChip file. Updated to read Affymetrix files from expression, genotyping, or resequencing assays on all platforms, except Solaris.

• celintensityread — Read probe intensities from Affymetrix CEL files. Updated to read Affymetrix CEL and CDF files from expression or genotyping assays on all platforms, except Solaris.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.6, the structure returned by affyread when reading a CHP file from an expression assay no longer contains a ProbePairs field. The ProbePairs field still exists in the structure returned by affyread when reading a CDF file.

Microarray Utility Functions

The following function is updated:

• probesetplot — Plot Affymetrix probe set intensity values. Updated to accept structures created from CEL and CDF files, instead of a structure created from a CHP file.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.5 and earlier, the probesetplot function accepted a structure created from a CHP file as input. Currently it requires two structures: one created from a CEL file and one created from a CDF library file. If you have any scripts that call the probesetplot function, you need to update them to provide the correct input arguments.

Microarray Normalization and Filtering Functions

Following is a new function:

• zonebackadj — Perform background adjustment on Affymetrix microarray probe-level data using zone-based method.

Mass Spectrometry Functions

The following function is updated:

• mzxmlread — Read mzXML file into MATLAB as structure. Updated to read mzXML files that conform to the mzXML 2.1 specification or earlier specifications.

Following is a new function you can use to calibrate and/or synchronize multidimensional mass spectrometry data:

• samplealign — Align two data sets containing sequential observations by introducing gaps.

Demos for Mass Spectrometry Functions

The following are two new mass spectrometry demos:

• Visualizing and Preprocessing Hyphenated Mass-Spectrometry Data Sets for Metabolite and Protein/Peptide Profiling

• Differential Analysis of Complex Protein and Metabolic Mixtures Using Liquid Chromatography/Mass Spectrometry (LC/MS)

Version 3.0 (R2007b) Bioinformatics Toolbox Software

Version 2.5 (R2007a) Bioinformatics Toolbox Software