E-MTAB-6694 - A microarray meta-dataset of prostate cancer

Status
Submitted on 1 January 2018, last updated on 10 April 2019, released on 11 April 2019
Organism
Homo sapiens
Samples (237)
Array (1)
Protocols (6)
Description
We present a meta-dataset comprising of a total of 237 samples including both primary tumors and tumor-free prostate tissues from six independent GEO datasets. To minimise inter-platform variation, only datasets generated from the GPL570 platform (Affymetrix Human Genome U133 Plus 2.0 Array) were processed to develop the meta-dataset. Using multiple open source R packages implemented in our previously developed bioinformatics pipeline, each dataset has been preprocessed with RMA normalisation, merged, and batch effect-corrected via Combat method. With increased sample size, the present meta-dataset serves an excellent 'discovery cohort' for discovering differentially expressed in diseased phenotype.
Experiment types
transcription profiling by array, disease state design
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-6694.idf.txt
Sample and data relationshipE-MTAB-6694.sdrf.txt
Processed data (1)E-MTAB-6694.processed.1.zip
Array designA-AFFY-44.adf.txt
Links