Brain Disease Correlation Analysis Project

• Fall 2016 Bioinformatics class project
• Final Report

RESOURCES

• 2-page proposal
• Microarray data analysis introduction (PH525x)

Facts worthy of attention

• Some incorrect expression values in GSE are transformed into null in GDS. Although GDS (Datasets) uses GSE (Series) as data sources, some expression values are different from GSE. In other words GDS is "curated" by The GEO team. So GDS is much helpful for determining which rows to be used.
• Some GDS needs do.log2=TRUE, and others need do.log2=FALSE. NaN in your expression values might be due to multiple log2 transformations.
• getGEO() might return partial .tar.gz files without any warnings. Using locally-cached files is strongly recommended.
• Some probe IDs of GPL570 and GPL96 are common. Comparison might be possible.
• There seems to be no 1-to-1 maps between Affymetrix Probe IDs and various types of gene IDs. I tried Entrez Gene ID, Ensembl ID, and Gene symbols. All failed. The better way might be to use Affymetrix Probe IDs as is.