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Matching of clinical cases to microarray samples was aided by using Unix scripts.
Immunohistochemistry on breast tumor tissue microarray samples was performed exactly as previously described [ 16].
Information for microarray samples was retrieved from NCBI's GEO database [ 49].
For each cell type, a large number of microarray samples was obtained, with no fewer than 118 samples for any one cell type (Additional file 5).
For in silico validation of the genes, a database containing processed GEO microarray samples was established as described earlier (Gyorffy and Schafer, 2009).
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Microarray samples were taken from similar plants at 40 days after sowing ns not significant *p ≤ 0.05 (significant); **p ≤ 0.01 (significant) based on t tests between means of genotypes within sampling dates and P levels.
In Figure 2, dimensional anchors (DA) representing each of the six microarray samples were positioned manually around the circumference of a circle such that iron-limited samples are on the left, samples with excess iron are on the right, and the vertical placement corresponds to the culture's transition from exponential growth (bottom) to stationary phase (top).
Tissue microarray samples were constructed at the Pathology Institute of the Charité Medical University Berlin.
Eight microarray samples were normalized by the RMA method of R affy package [ 41].
This result indicates that all microarray samples were successfully labeled, hybridized, and scanned.
Microarray samples were analyzed using dChip [ 82] and BRB Arraytools [ 83], as described previously [ 17].
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