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ChIPed DNA was measured by real-time PCR in duplicates and the median of the average Ct values of all the amplicons in each sample was scaled to 22.
Each sample was scaled to a target intensity of 500 for all probe sets.
Each sample was scaled to a target intensity of 1000 using the "all probe sets" scaling option, this option scales the trimmed mean target intensity to the specified value [ 11].
In both cases, the rank of each sample was scaled by the number of samples in the cohort, so that for each cohort the data is in the range zero to one.
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The bias error for the recursive sample is scaled by (h_{hat {x}_{b}}), and the residual noise term is scaled by (h_{hat {x}_{n}}).
As the normative sample is scaled to a mean of 50 and standard deviation of 10, we believe the sample to be representative of the general population.
The pixel size on the sample is scaled by the optics too; by the ×15 Cassegrain objective/condenser, the effective pixel size over the sample (i.e. optical sampling) is 2.6 μm.
Raw read counts of a new patient sample were scaled using previously stored quantitative preprocessing information from the reference cohort, thus being the geometric mean of the counts from each gene across all samples in the reference cohort.
Both data sets (van de Vijver and BBCP) are preprocessed and clustered as follows: The logarithms of ratios between the respective gene expression to reference sample are scaled to [-1, 1].
In the case of dataset GSE3325 each signal intensity from the primary tumour samples was scaled to the corresponding median gene signal intensity across the benign tumour samples.
The input samples were scaled into the [0,1] range using the global minimum and maximum of the data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com