DEGseq MA-plot red points

[Zhe]

Hello,

I used the function "DEGexp" with the method MARS to generate a MA-plot. Do the red points represent the differentially expressed genes with P-value < 0.001?

Thanks,
Zhe

[Xi Wang]

Hello,

I used the function "DEGexp" with the method MARS to generate a MA-plot. Do the red points represent the differentially expressed genes with P-value < 0.001?

Thanks,
Zhe

Hi, sorry for the late reply.

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).