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  • The effect of normalization on asymetrically DE genes

    Hi All,
    We are studying a transcriptional repressor protein by comparing the WT to a strain lacking that repressor in an RNAseq experiment. Because the protein is a repressor, most of the DE genes are upregulated. It seems that many normalization techniques rely on an assumption that the ratio of upregulated and downregulated genes is approximately equal. Does anyone have any advice for dealing with this asymmetry, or is this a non-issue?

    Any advice or links to relevant threads I failed to find would be appreciated; thanks in advance!

    EDIT: To clarify, i have uploaded an image of an MA plot to show the asymmetrical distribution.
    Last edited by nw328; 09-21-2015, 08:05 AM. Reason: add picture

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