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All tissues used for downstream studies were prospectively randomized during processing and sectioning, prior to expression analysis, to minimize technical batch effects in the data.
A comparison of patient characteristics based on phenotypic group can be found in Additional File 3. Notably, we ensured that the patient samples in the training cohort were all processed together to minimize technical batch effects.
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To minimize technical variability, target synthesis and hybridizations were done in batches of 6 where all treatment groups were equally represented.
To minimize technical variability, all targets were synthesized in one round and hybridization experiments were conducted on slides from a single batch.
To minimize technical variability, all targets were synthesized in one round and each hybridization experiment was conducted simultaneously on slides from a single batch where possible.
This helped minimize technical noise associated with oligodeoxyribonucleotides labeling efficiency.
This selection procedure was performed twice to minimize technical errors and false positives.
Reciprocal dye swap replicate hybridizations were performed to minimize technical noise.
An effective normalization technique should minimize technical and experimental bias without introducing noise.
We applied stringent quality control and filtering procedures to minimize technical variation.
We anticipate that the use of vault nanoparticles will circumvent autologous DC preparation, minimize batch to batch variability and allow for comparability and standardization.
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