DNA Array Data Analysis

The following software packages for gene expression analysis are available through the Core:

  • Expression Console
  • Transcriptome Analysis Console
  • Ingenuity Pathway Analysis

Extensive consultation with Core Facility staff for technical and bioinformatics support will carry a consultation fee of $50/hour. Ingenuity Pathways Analysis (IPA) is currently accessible at a charge of $250/month, until our current license expires on December 6, 2017. Analysis of data not generated by the Core Facility requires prior permission by the Core Facility to use IPA.  IPA may only be accessed through one computer located in the Research Core Facility.

Transcriptome Analysis Console (TAC) is available as a free download from ThermoFisher.  It is only compatible with a Wiondows operating system and requires a minimum of 8GB of RAM.  TAC is installed in the RCF Computer Lab.

The following data files will be delivered to the investigator:

  • Experiment File *.ARR: This file contains the parameters of the experiment such as probe array type, experiment name, equipment parameters and sample description. This file is not used for analysis, but may be needed to open other files for the designated chip experiment.
  • Image Data File *.DAT: This is an image file generated after scanning the array. This file can be opened in some viewer packages to assess the quality of scanning. It is used in Expression Console to generate the *.CEL file.
  • Image File *.JPG: This is a snapshot of the .DAT file.
  • Cell Intensity File *.CEL:  This binary file is the result of low level analysis performed from the *.DAT image file. It is can be used as for further analysis.
  • Probe Array Results File *.CHP: This is a gene level summarization of the CEL file using the Affymetrix’ normalization algorithms. It is exported from Expression Console. It can also be used as the base file for further analysis; however, there are many other algorithms that have been adopted by the scientific community other than those provided by Affymetrix software, hence the reason why CEL files are often preferred over CHP files for analysis.
  • Report File *.RPT: The report file is generated from the CHP file. This expression report summarizes information about expression analysis settings and probe set hybridization intensity data.
  • Audit File *.ADUIT: The audit file is an XML file that tracks the processing of each physical array processed by AGCC. An audit file is produced for each physical array and tracks all the processing steps that were performed on the array, including multiple scans and regridding.

In addition to the files above, intensity values will be provided in an Excel spreadsheet. Upon request, the LSUS bioinformatics team can provide help with specific needs.

LSUS Bioinformatics Team

Dr. Marjan Trutschl
Office: Technology Center 216
Marjan.trutschl@lsus.edu
318-797-5131 (office)
318-795-4274 (research lab)

Dr. Urška Cvek
Office: Technology Center 215
Urska.cvek@lsus.edu
318-795-4266 (office)