Seasoned clinicians also consider the age of the patient, tumour grade and perhaps the semi-quantitative ER, progesterone receptor and Ki67 expression values that each influence to a variable extent the risk of recurrence and endocrine sensitivity.
For example, a chromosome can be broken into consecutive, non-overlapping, 100 megabase (Mb) intervals and gene expression values that map to each interval tested for an expression biases using a variety of statistical/computational approaches.
Gene expression cutoff values that best segregated patients into poor- and good-response subgroups were defined by using the maximal χ method.
Once probes have been introduced into the system, experimental data is inserted by selecting a term in the ontology and uploading the expression values that are automatically linked to the backend database through probe names.
The resulting data set was cleaned and processed to include only the expression values that (a) differed by 20% between duplicates, and (b) for which data were obtained from at least 80% of the specimens.
We provide evidence that the Stage I pre-processing algorithms considered in Dabney and Storey fail to provide expression values that are adequately centered or scaled.
It is expected that RNA-Seq methodologies will supersede microarrays for transcript profiling because of higher sensitivity, base-pair resolution and the larger range of expression values that can be detected [ 3, 5, 9].
Instead, the t-test was applied to identify those genes with expression values that differ significantly between normal and tumour samples (for HTM and Oncogenomics datasets) in each cancer model.
We identified all expression values that were more than 3.4644 standard deviations from the mean expression value for that particular transcript (see methods for an explanation for choosing this threshold).
To overcome this shortcoming, an outlier removal step is performed before the F-test, to eliminate those expression values that are significantly higher or lower than majority of the expression values.
