Supplementary Microarray Data


Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics. 2004 Nov 22;20(17):3166-78.

Data Sets

This paper introduces a novel method for combining data from multiple microarray platforms. We applied the method to data from three studies of CLL. Two of the studies were carried out elsewhere:
  1. Lymphochip glass array data from the publication by Rosenwald et al. is available from the Stanford Microarray Database. To find the data, it's probably best to limit the organism to Homo sapiens and sort by author.
  2. Affymetrix array data from the publication by Klein et al. was obtained by contacting the senior author, Riccardo Dalla-Favera. directly.

The third data set was produced a few years ago in the laboratory of Dr. L.V. Abruzzo. This data set consists of microarray data on 12 samples (6 from CLL patients, 6 from peripheral blood B cells from normal controls). The experiments were performed on Research Genetics nylon microarrays, using radioactively labeled target samples. Following standard practixe at the time, each membrane was stripped and re-used in multiple experiments. Our paper describing sources of variation on nylon membrane arrays found that membranes could be safely reused up to four times. Each Research Genetics nylon microarray contained 5760 spots; a complete set of 6 different microarrays provided genome-wide coverage, using a total of more than 30000 cDNA clones.

Processed nylon microarray data

Raw nylon microarray quantification data