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Notes and things to keep in mind¶

In terms of the meta-analysis¶

case/control vs other comparisons

use provided normalized data as a first pass

study level covariates: age, gender, smoking, race

meta-analysis of p-values or exp. ratios should include disease state and laboratory as a co-variate

Potential issues¶

are there sample ids that go across studies

need to ensure that a sample is not used twice

GEO file types¶

GEO Platform (GPL) - These files describe a particular type of microarray. They are annotation files.

GEO Sample (GSM) - Files that contain all the data from asingle chip. For each gene there will be multiple scores including the main one, held in the VALUE column.

GEO Series (GSE) - Lists of GSM files that together form a single experiment.

GEO Dataset (GDS) - Curated files with a combination of a GSE file and its GSM files. They contain normalised exp. levels for each gene from each sample (i.e. just the VALUE field from the GSM file).

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