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General Departmental Seminar Series

An experience with cDNA arrays: traps for the unwary

Terry Therneau, Section of Biostatistics, Department of Health Science Research (work co-authored with Diane Jelinek, Department of Immunology), Mayo Clinic

Wednesday, October 20, 1999, 4:00 p.m.

1221 CSSC, 1210 W. Dayton St.


I will give an overview of our experience with the application of one particular set of cDNA arrays (Research Genetics) to a set of patient derived multiple myeloma cell lines. The main goal of the experiments is to understand the effect of IL-6 on cell dynamics, but the majority of the analysis has been concerned with data standardization and quality control. We have looked at the following issues:

  • The spatial layout of the data, and systematic variation within the array (spatial correlation)
  • Bleed-over between adjacent areas, in the reading of the array
  • The utility and placement of control spots
  • Normalization of two or more arrays to a common intensity
  • Setting a lower threshold
  • Highlighting functional changes in expression versus noise

Proper normalization of the final data is absolutely key to their usage for anything except the detection of huge (>4 fold) changes in expression. I will finish with some ideas for how this might be accomplished in the face of the problems described above. This is an area with lots of room for further ideas and research.

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