Process Description
Bioconductor Expresso for Affymetrix Wrapper
The BioConductor Expresso process functions as a wrapper around the expresso function in BioConductor.
What do I need?
You must download and install both the current R and Bio C packages from the BioConductor website before using this process. Make note of the location of the Rterm.exe file. The location of this executable, which is required to submit R programs in batch mode, must be specified.
BioConductor Expresso in JMP Genomics 5.1 requires one of the following combinations:
| • | R version 2.6.2 and the BioConductor version 2.1, |
| • | R version 2.8 and the BioConductor version 2.3, |
| • | R version 2.9 and the BioConductor version 2.4, or |
| • | R version 2.11 and Bioconductor version 2.6. |
In addition to the software, you must also download and install the proper BioConductor package, including the library packages for the specific arrays. These can be downloaded from the BioConductor website .
In order to import data using the BioConductor Expresso for Affymetrix process, you must have a set of files, either .chp or .cel files containing the raw data and an existing JMP Genomics Experimental Design File (EDF). These files should all be saved to the same folder. A typical .cel file, opened using a text editor, is shown below.
The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet, and must be created before the data can be imported. At a minimum, the EDF must contain three columns:
| • | A column named Array or Chip, whose entries identify the specific chips in the experiment, |
| • | A column named File or FileName, whose entries identify the files containing the raw data, and |
| • | A column named ColumnName whose entries correspond to the variable names in the SAS data set to be generated. |
The exp.xls file (opened in JMP) is shown below.
The following example uses the GSE1155 public data set downloaded from the Gene Expression Omnibus (GEO). This data set, composed of eleven .cel files, represents the results of expression profiling of brain hippocampi of rats fed a ketogenic diet. Files were downloaded and saved to the GSE1155 folder (created in the JMP Genomics Sample Data directory). The contents of this directory are shown below.
The required Experimental Design File (EDF) was generated using the Create a Design Data Set from an Existing Data Set process and saved as the exp.xls file. This file contains one row for each .cel file and all of the required columns.
In this example, we use default settings to carry out background noise correction, normalize values across all eleven arrays, carry out perfect match probe adjustments, and compute summarized expression values.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Output/Results
The output data sets generated by this process are listed in a Results window. Refer to the BioConductor Expresso for Affymetrix Wrapper output documentation for detailed descriptions.