tissue: breast cancer hr: 1 her2: 0 mp: 1 pcr: 0 arm: Ganitumab Arm
Extracted molecule
total RNA
Extraction protocol
Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL16233.
Label
Cy3
Label protocol
Performed by Agendia Inc (Irvine, CA)
Hybridization protocol
Performed by Agendia Inc (Irvine, CA)
Scan protocol
Performed by Agendia Inc (Irvine, CA)
Data processing
gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515]. The data matrix for this study constitutes 233 samples from this larger COMBAT-combined expression set. Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 233 samples for batch correcting on raw files. The linear adjustment factors and updated probe annotation files per platform are provided. The data matrix provided contains platform corrected, normalized expression values from two different platforms. Data is collapsed on the gene level as was used in the analysis.
