TY - JOUR
T1 - Retriever and CompareTable, two informatics tools for data analysis of high-density oligonucleotide arrays
AU - Brasier, Allan R.
PY - 2002
Y1 - 2002
N2 - 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®).
AB - 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®).
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U2 - 10.2144/02321bc01
DO - 10.2144/02321bc01
M3 - Article
C2 - 11808683
AN - SCOPUS:0036138971
SN - 0736-6205
VL - 32
SP - 100
EP - 109
JO - BioTechniques
JF - BioTechniques
IS - 1
ER -