Retriever and CompareTable, two informatics tools for data analysis of high-density oligonucleotide arrays

Allan R. Brasier

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

High-density oligonucleotide arrays are widely employed for detecting global changes in gene expression profiles of cells or tissues exposed to specific stimuli. Presented with large amounts of data, investigators can spend significant amounts of time analyzing and interpreting this array data. In our application of GeneChip® arrays to analyze changes in gene expression in viral-infected epithelium, we have needed to develop additional computational tools that may be of utility to other investigators using this methodology. Here, I describe two executable programs to facilitate data extraction and multiple data point analysis. These programs run in a virtual DOS environment on Microsoft® Windows® 95/98/2K operating systems on a desktop PC. Both programs can be freely downloaded from the BioTechniques Software Library (www.BioTechniques.com). The first program, Retriever, extracts primary data from an array experiment contained in an Affymetrix® text file using user-inputted individual identification strings (e.g., the probe set identification numbers). With specific data retrieved for individual genes, hybridization profiles can be examined and data normalized. The second program, CompareTable, is used to facilitate comparison analysis of two experimental replicates. CompareTable compares two lists of genes, identifies common entries, extracts their data, and writes an output text files containing only those genes present in both of the experiments. The output files generated by these two programs can be opened and manipulated by any software application recognizing tab-delimited text files (e.g., Microsoft NotePad® or Excel®).

Original languageEnglish (US)
Pages (from-to)100-109
Number of pages10
JournalBioTechniques
Volume32
Issue number1
StatePublished - 2002

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Informatics
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Software
Research Personnel
Genes
Gene expression
Transcriptome
Epithelium
DOS
Computer operating systems
Gene Expression
Application programs
Experiments
Tissue

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Retriever and CompareTable, two informatics tools for data analysis of high-density oligonucleotide arrays. / Brasier, Allan R.

In: BioTechniques, Vol. 32, No. 1, 2002, p. 100-109.

Research output: Contribution to journalArticle

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