Land normalization of expression data

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Overview

Nearly all microarray expression data in OmicSoft Lands are re-processed from the signal intensity files in GEO/ArrayExpress, and normalized to improve cross-project comparisons.

Affymetrix Microarrays

Affymetrix expression data are reprocessed from raw .cel files, obtained from GEO or ArrayExpress; please see Omicsoft Affymetrix Microarray Preprocessing for details of normalization. The intensities are then scaled so that the median probe is at a target intensity of 500 for each sample.

Illumina/Agilent Microarrays

Signals are extracted from source files (GEO or ArrayExpress). In general, these have been pre-background subtracted, so additional background correction is not performed (case-by-case exceptions with unusual normalizations will be reprocessed by OmicSoft). Intensity values are re-scaled so the median probe value is 500 in each sample.

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