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ZW-xjtlu / exomePeak2

Peak calling and differential methylation for MeRIP-Seq
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output padj with many NAs #8

Open sunhaifeng123 opened 3 years ago

sunhaifeng123 commented 3 years ago

Hi, ZhenWei:

The R package exomePeak2 is nice and ideal for m6A-Seq analysis in our group.

But recently a result troubled me:

In the Differential Modification Analysis result: DiffMod.xlsx, the padj column have many NA. And the corresponding pvalue rank from 0.00000135 to 0.999901024.

I dont konw how to deal with these peaks, can you help offer some help?

And a minor question:

What does the DiffModLog2FC mean, it seems derived from "ModLog2FC_treated-ModLog2FC_control" or like log2(IP.Treated/IP.Control) ?

And in your group, waht's the better parameter cutoff for Differential Modification Peaks? pvalue or padj 0.05, and should a cutoff on DiffModLog2FC?

Thank you in advance for your reply!

Haifeng Sun Nanjing Medical University, Jiangsu Province

The supplementary materials was emailed to you (Zhen.Wei01@xjtlu.edu.cn).

Thanks again!

JieqiangHe commented 3 years ago

If you solve it, please lets me know ! thx a lot!

wangyuhu123 commented 9 months ago

Have you solved this problem?