Originally posted by Zhe
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Yes, the red points are the genes identied as dierentially expressed. And you can specify the criteria for DEGs by combining the options in "DEGexp" below:
pValue
pValue threshold (for the methods: LRT, FET, MARS, MATR). only used when thresholdKind=1.
zScore
zScore threshold (for the methods: MARS, MATR). only used when thresholdKind=2.
qValue
qValue threshold (for the methods: LRT, FET, MARS, MATR). only used when thresholdKind=3 or thresholdKind=4.
thresholdKind
the kind of threshold. Possible kinds are:
• 1: pValue threshold,
• 2: zScore threshold,
• 3: qValue threshold (Benjamini et al. 1995),
• 4: qValue threshold (Storey et al. 2003).
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