Question: Extracting normalized counts in MEDIPS
0
24 days ago by
lshepard20
United States
lshepard20 wrote:

Hello,

Just a simple question about the package MEDIPS. I have found this to be a great source fo MeDIP-seq, however, one point which is bugging me is that the counts present in the resulting file is not the TMM normalized counts used for differential coverage testing (for the MEDIPS.meth functions. Is anyone aware of how I can extract the normalized values?

Thanks!

medips medip-seq • 37 views
modified 24 days ago by Lukas Chavez510 • written 24 days ago by lshepard20
Answer: Extracting normalized counts in MEDIPS
0
24 days ago by
Lukas Chavez510
USA/La Jolla/UCSD
Lukas Chavez510 wrote:

Hi Ishepard,

Thank you for your positive feedback about MEDIPS! Unfortunately, the implementation does not allow to output TMM normalized counts. The fold change, group-wise mean and p-values are all calculated based on the normalized counts, though.

To also output library size normalized counts it would be necessary to edit the MEDIPS.diffMeth and MEDIPS.meth functions. However, there are no plans on our side to do so. Instead, I recommend to look into our new package qsea! It might not be as straight forward to use as MEDIPS, but is much more flexible on the other side.

All the best, Lukas