Question: What does DESeq2 non symmetric MA plot mean in differential analysis?? (hi-chip)
1
gravatar for woongjaej
4 weeks ago by
woongjaej20
woongjaej20 wrote:

Hi, I'm a researcher using DESeq2 for hi-chip differential analysis.

When I performed differential analysis using DESeq2, I found that my data's MA plot is far non-symmetric.(Even for not significant values)

I thought it can happen because it's not RNA-seq data. But I can't explain exactly why.

non symmetric MA plot example for my hi-chip data I have three questions here.

  1. Does someone know what's the meaning of non-symmetric MA plot in DESeq2 for the data? Can this happen or should I think my data is not good?
  2. If non-symmetric MA plot like this is not good, can I make it symmetric???
  3. Can I use DESeq2 for differential loop analysis??(My data's coverage is similar between samples)

Thank you for your help.

ADD COMMENTlink modified 4 weeks ago by ATpoint46k • written 4 weeks ago by woongjaej20

A couple of points:

  1. The Tool type post is for advertising/speaking about tools, not for Questions concerning tools. The category for that would be the Question category.
  2. Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)
ADD REPLYlink written 4 weeks ago by Ram32k

Oh, I see.

Thank you very much

ADD REPLYlink written 4 weeks ago by woongjaej20

Cross-posted at Bioc (it is good practice to link crossposts): https://support.bioconductor.org/p/p134337/

ADD REPLYlink written 4 weeks ago by ATpoint46k
2
gravatar for ATpoint
4 weeks ago by
ATpoint46k
ATpoint46k wrote:

This looks like trended bias. I would guess that actually the entire plot would need to be shifted like upwards along the y-axis by +1 and by this most of these 10307 would no logner be significant. I'd say that normalization is totally off here using the default size factor method from DESeq2 which does not (afaik) handle trended biases. The farright part of the plot, kind of the "arrowhead" of this plot is probably all non-DE. Take a look at diffHic, a method developed for differential HiC analysis that might be of interest here, especially the part about removal of trended biases which is section 5.2.1 in https://bioconductor.org/packages/release/bioc/vignettes/diffHic/inst/doc/diffHicUsersGuide.pdf

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by ATpoint46k

Oh, thanks a lot!

I'll look into diffHic.

Thank you very much

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by woongjaej20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 953 users visited in the last hour
_