Labeling of probes, hybridization of slides and scanning was done essentially as described [Petersen, D. et al. BMC Bioinformatics 6, 63. 2005]
Scan protocol
Slides were scanned using an Axon 4000B instrument at 10 micron resolution. All scans were performed at 100% laser power, but the PMT setting varied from slide-to-slide depending on the labeling and hybridization outcomes. Thus, the intensity of the signals among the slides will vary, but the Cy3/Cy5 ratios will be much less variable.
Description
NCI sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5). This is the second (and different) printing of the NCI.
Data processing
Images were processed and quantified using GenePix 4.0 or higher software (Axon Instruments, Union City, CA). The data were filtered (or flagged) on the basis of signal levels and spot quality. The raw data were submitted to MAQC and further normalized by using median-scaling and LOWESS.
