Revision as of 16:34, 11 March 2011

Overview

This chapter covers:

• Data file formats supported by geWorkbench
• Loading microarray data from local files, while merging the data into one data set.
• Merging data from several previously loaded microarray experiments.

Open File Dialog

The Open File dialog can be reached in two ways:

• Right-click on a Project and select "Open file(s)".
• From the top-level menu bar, select File->Open->File.

The selector lists the available file types that geWorkbench can load. Once a file type is chosen, only files matching the indicated file extension, e.g. (*.exp, *.fasta etc.) will be displayed in the available file list.

The file browser offers standard options

• Select Directory - A pulldown of directories available at the current directory level. The contents of the directory are listed below when a directory is selected.
• Up One Level - Move up one directory level.
• Desktop - Go to the user's desktop or home directory.
• Create New Folder - create a new directory in the current one.
• List - Display only the names of files and directories contained in the current directory.
• Details - Display name, size, type and date of items in the directory.

Supported data formats

• Adjacency Matrix - An interaction network such as generated using ARACNe.
• Affy .CEL files - Affymetrix CEL files (probe level data) can be viewed graphically in geWorkbench but not used directly for analysis.
• Affymetrix File Matrix - a geWorkbench spreadsheet-type multi-experiment format; this is the native file type created by geWorkbench from merged datasets. It can contain the data from any number of arrays in a spreadsheet-like "matrix" format. It also allows for the grouping of arrays into named subsets based on phenotypic criteria. Multiple such groups can be defined, each containing a different division of the arrays among named sets. geWorkbench can create files in this format from data read in in other formats.
• Affymetrix MAS5/GCOS files - produced by Affymetrix data analysis programs.
• FASTA files. DNA or amino-acid sequence files in FASTA format.
• Genepix .GPR files - Produced by a popular analysis program for two-color microarrays.
• GEO Soft and GEO Series formats
  • GSM - individual sample files.
  • GSE - series files representing an entire experiment, e.g. GSE2189_family.soft.
  • GDS - curated data matrix, e.g. GDS507_sample.soft.
  • Series matrix - matrix format of submitted, uncurated data, e.g. GSE2189_series_matrix.txt.
• MAGE-TAB data matrix - this is an auxiliary MAGE-TAB data file type that can be used to contain summarized data from multiple arrays.
• PDB Structure File - Molecular structure in Protein Data Bank format.
• Tab-delimited text (e.g. files exported by RMAExpress or other programs) - A simple columnar file format.

Microarray Annotation files

• Affymetrix standard annotation files, in CSV format. See File_Formats#Annotation_Files for further details.

=Other

• PDB files - protein 3-dimensional structure files can be viewed in the JMol Viewer in geWorkbench.
• NetBoost Edge List - used by a component still under development.

Detailed expression file formats

Several of the expression file formats are described in detail on File Formats page.

Microrray data and merging datasets

When working with microarray data, all data to be analyzed must be present within one data node in a project. If the data exists as multiple files containing results from single arrays, the data must be merged into a single node before it can be used. geWorkbench can perform this merging step either at the time data is read in, or later in a separate step. Once merged, such a dataset can be saved to disk; it will be saved in the geWorkbench matrix file format.

Tutorial: Loading microarray data files - local

In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset. The origin of these file is described in the section Tutorial_-_Data.

Note that no Affymetrix annotation files are included in the geWorkbench distribution. The annotation file for the HG-U95Av2 array used in this example can be obtained from the Affymetrix website. See the instructions in the FAQ entry on this topic.

1. Right-click on the default Workspace entry in the Project Folders component.

2. Next, right-click on the new Project entry and select Open Files.

A file browser will appear with which you can select the files you wish to open. The default is to browse for local files, that is on your own computer. geWorkbench can also access data from caArray databases (the Remote option).

3. Here, we select the file type Affymetrix GCOS/MAS5 as shown.

4. Make sure to check the Merge files checkbox. This will create the merged data node as the files are read in.

5. We will select 10 MAS5 format text files from the directory data/cardiogenomics.med.harvard.edu, which is included within the geWorkbench installation.

6. Click Open.

A message will appear giving information about associating an annotation file with the dataset.

7. A file browser will then open with which you can, if you wish, select an annotation file matching your dataset. This is needed if you intend to use features of geWorkbench such as the Sequence Retriever or GO Terms component (Gene Ontology).

A status bar will display as the data is loaded:

8. The merged data set is listed in the Project folder. The individual arrays are shown below in the Arrays component.

Note - if you have created a custom Affymetrix-format annotation file which has more than one entry for a probeset, an error dialog will be shown.

See File_Formats#Affymetrix_Annotation_Files for further details.

Tutorial: Merging microarray data files after they have already been loaded.

If data files are not merged at the time they are read in, they can also be merged later, as long as they are from the same chip type.

1. Select the read-in data files that you want to merge.

2. Click on File in the menu bar, and choose Merge Datasets.

3. The result is a new data node containing the merged data. The original data nodes are still present.