Paired microRNA-mRNA dataset " Array-based bioinformatic analysis on pediatric primary central nervous system germ cell tumors"[ 24] has been selected to test linear model assumptions.
The diagonal gives the original dataset dimensions (array mutants × query mutants).
Batch effects of dataset, plate, array and position were removed using ComBat [ 43].
Transcriptome profiling and differential gene expression analyses traditionally use microarray technology, which requires cDNA library, Expressed Sequence Tags (EST) dataset and array hybridization.
The bladder carcinoma dataset contains array-CGH profiles with 2143 probes on non-sex chromosomes.
The uveal melanoma tumor dataset has array-CGH profiles with 3649 probes on non-sex chromosomes.
Thus performance of the signature is robust across different datasets and array platforms.
For Datasets 1 3 array images were processed using Agilent Feature Extraction software version A.6.1.1.
The method first learns the model's parameters on a training dataset of array-CGH sequences with known sequence labels.
This series reflects the most complete version of the dataset (46 arrays, as used in Additional file 4).
For the Bild dataset, replicate arrays from each of the five mutation pathways were compared to control GFP-treated tissue profiles.
