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gilesc / gseconvert

Constructs and preprocesses a gene expression matrix from raw GSEs for use in meta-analyses
http://corygil.es/
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Criteria for exclusion during GSE processing #10

Open mdozmorov opened 13 years ago

mdozmorov commented 13 years ago

Exclude GSM, if, • mean or median equal to 0 (weird distribution, suspects for ratio) • mean to median ratio equal to or less than 1.2 (suspects for ratio) • negative values present Consider: • Mean =>7 and <=16 – need to be unlog2 transformed • >1% missing should be done AFTER removing genes appearing in 0 experiments

gilesc commented 13 years ago

log2 transform and ALL values must be negative fixed: e6b06da0bdb850dc3098

Exclude 1% missing still needs to be done (and is of course only applicable to platform-specific matrices)