This page contains supplementary material for:

Correction of technical bias in clinical microarray data improves concordance with known biological information
Aron Charles Eklund and Zoltan Szallasi
Genome Biology 2008, 9:R26

Abstract: The performance of gene expression microarrays has been well characterized using controlled reference samples, but the performance on clinical samples remains less clear. We identified sources of technical bias affecting many genes in concert, thus causing spurious correlations in clinical data sets and false associations between genes and clinical variables. We developed a method to correct for technical bias in clinical microarray data, which increased concordance with known biological relationships in multiple data sets.

The authors are in the Cancer systems biology group at CBS.

Publication links:

• Genome Biology
  
• PubMed record
  

The R package bias for correction of technical bias

• Source package: bias_0.0.5.tar.gz
• Windows package: bias_0.0.5.zip
• Older packages are here.
  

Links to raw data unavailable from GEO:

• Breast cancer (Signoretti et al.)
  

R code to reproduce results:

• script 01 generates figures 1-4.
• script 02 generates figure 5.
• script 03 generates figure 6.
• script 04 generates additional data file 1.

Raw data ("AffyBatch" objects in R data format):

• Signoretti(breast cancer, 89 MB)

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