MAnorm output

[catch-minie]

I have a question regarding results of MAnorm , the result contains following header :
chr start end description #raw_read_1 #raw_read_2 M_value_rescaled A_value_rescaled -log10(p-value)

I want to know the detail about column raw_read1 & raw_read2 , what does it refers to?

[ying-w]

Using bedtools intersect bed to count how many reads overlap each region as defined by the bed file. This would be the raw counts that get fed into the MA adjustment.

[catch-minie]

And Wat is the MA adjustment ?

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On 04-Jan-2017, at 7:13 PM, Ying ***@***.***> wrote: Using bedtools intersect bed to count how many reads overlap each region as defined by the bed file. This would be the raw counts that get fed into the MA adjustment. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[ying-w]

have a look at either the original paper or my comparison paper

the main idea is assuming shared peaks are non-differential and normalizing all peaks to shared peaks. This assumption sometimes holds and sometimes doesn't depending on what kind of cells are being compared.