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molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
https://github.com/molgenis/systemsgenetics/wiki
GNU General Public License v3.0
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Centering of expression data #304

Open PatrickDeelen opened 10 years ago

PatrickDeelen commented 10 years ago

The expression data is not centered at the mean before calculation of the correlation. The used correlation function requires that this is the case. Although usually this will not change the result as long as the genotypes are centered @ludefranke suggest to fix this just to be sure.

Note: this must be done after removing expression of samples with missing genotypes

Bonder-MJ commented 10 years ago

This is only fixed for the normal metaQTL runs. Potentialy not for the special cases, @harmjanwestra could you check this?