Array CGH Tools

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This site provides technical protocols, tools, and microarray data sets. Use of technical protocols and analysis tools from this site is intended for academic non-commercial use only by not-for-profit academic institutions. For commercial uses or all other uses by for-profit entities, please contact Office of Research and Technology Ventures (ORTV) at Dana-Farber Cancer Institute.

• Labeling Protocols
1. aCGH Labeling Protocol
2. aCGH Oligo Labeling Protocal


• Analysis Tools
1. Analysis and mapping tools by Dr. Cameron Brennan . Please read the install instruction.
2. cghMCR - an R package (finds regions of gains or losses across samples) submitted to BioConductor with instructions.
3. CNTools - an R package (converts segmented data into a feature by samples foramt) submitted to BioConductor with instructions.
4. Agilent - an R package for normalizing arrayCGH data (Agilent.tar. Agilent.zip)


• Microarray data sets
  • Glioblastoma
    1. Human primary vs secondary GBM (FFPE)
  • Lung cancer
    1. cDNA
    2. Agilent 22k array CGH
    3. AffyMatrix U133a plus2 array
  • Multiple myeloma
    1. Agilent 22k array CGH
  • Pancreas cancer
    1. ACGH on cDNA array
    2. Affymetrix U133A profiles for 26 cell lines
  • Other
    1. Long oligonucleotide

Disclaimer: The user of this website agrees that the analytical tools available on this site are provided AS IS, are experimental in nature, and are provided WITHOUT ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR USE. DFCI MAKES NO REPRESENTATION AND PROVIDES NO WARRANTY THAT THE USE OF THE WEB SITE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.