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Thus, over one-fourth of all of the genes assessed on the microarray were differentially expressed (i.e. q-value of <5% in multi-class significance analysis of microarrays (SAM)) between at least two conditions.
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The quality of the microarray data was assessed on the basis of a report from the arrayQualityMetrics package [ 26] and by observation of the distribution of the log2 intensities on each array before and after normalization (Additional file 1A).
The inter-observer variability of TOPK scores was assessed on one tissue microarray slide containing 456 cases by a second independent pathologist (MH) from an external institution and blinded to clinicopathological features.
No penalty was assessed on the play.
No penalty was assessed on the hit.
Each of the spiked pools was assessed on duplicate microarrays.
To extend our findings, we utilized a cohort of patients from the Nurses Health Studyy (NHS) with ER/PR data recorded in the medical record and assessed on tissue microarrays (n = 2,011).
For resected specimens, an average of 3 × 1.6 mm cores were assessed on tissue microarrays; however, due to limitations in tissue availability, only one or two cores were assessed for biopsy specimens.
A total of 36 DR0401-restricted epitopes derived from hemagglutinin (HA), neuraminidase (NA), nuclear protein (NP), polymerase B1 (PB1) and M1 matrix protein (MP) were assessed on a single microarray simultaneously.
Tissue samples from 174 patients with a primary urothelial carcinoma were immunohistochemically assessed on a tissue microarray.
Caveolin-1 and CAV2 protein expression was assessed on a tissue microarray containing 880 unselected invasive breast cancer cases, by means of immunohistochemistry. Caveolin-1 and CAV2 expression was observed in 13.4 and 5.9% of all breast cancer, respectively.
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