6 protocols
normalization data transformation protocol
Normalized log2(ratio) profiles were segmented using DNAcopy, the R implementation of the CBS algorithm, with default parameters, except for undo set to undo.sd, and undo.SD set to 1 or 2 depending on the profile quality.
normalization data transformation protocol
Hybridizations were normalized for their dye type using limma's loess implementation in R. Data were transformed into log2(Cy5/Cy3). Resulting log2(ratio) profiles were normalized for their GC% content. Resulting profile was centered on the most probable normal level value. Profiles from reversed hybridizations (Test/Norm = Cy3/Cy5) were inversed.
array scanning protocol
Arrays were scanned using Agilent Scanner G2565CA, following the manufacturers protocol.
hybridization protocol
Cy3-labeled and Cy5-labeled DNA were pooled and hybridized to the SurePrint G3 Human CGH Microarray 2x400K (Agilent Technologies)
labelling protocol
Test DNA samples were labeled using Cy5 fluorescent dye. Reference DNA samples were labeled using Cy3 fluorescent dye, from Agilent Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturers protocol. For 2 hybs this pattern is reversed: hyb_S_12 and hyb_S_61. This is a technician error in sample naming, which was corrected a posteriori. It was detected by observing Cy5 and Cy3 signals : we observed that the Cy5 channel (corresponding to tumor) exhibited a flat profile, whereas the Cy3 channel (corresponding to patient's normal thyroid tissue) exhibited large-scale aberrations.
nucleic acid extraction protocol
DNA was extracted using Qiagen DNA extraction kit. No extraction was required for the reference samples as they were purchased as genomic DNA from Promega.