SEQanswers

Go Back   SEQanswers > Applications Forums > Epigenetics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MeDIP-seq data analysis paolo.kunder Bioinformatics 0 02-15-2013 04:21 AM
Problems with Medip-chip data analysis using batman chitra24 Epigenetics 1 01-14-2013 06:10 AM
meDIP-chip/meDIP-seq/MethylCap-seq using mouse DNA Jones90 Epigenetics 6 09-13-2012 11:00 PM
MeDIP-seq - input sample needed? ETHANol Epigenetics 4 12-23-2011 09:08 AM
MeDIP-seq versus ChIP-seq analyses? jjw14 Bioinformatics 8 08-24-2010 08:22 AM

Reply
 
Thread Tools
Old 03-11-2013, 08:23 AM   #1
rachita
Junior Member
 
Location: Boston

Join Date: Mar 2013
Posts: 7
Default MedIp-seq Input data

HI Everyone,

I am analysing MedIP-seq data from adipose tissue and there are control and treated samples. But there is no "INPUT SET" available. Is there any way I can get the analysis done without the input set. Can I use the control data as INPUT set ?
rachita is offline   Reply With Quote
Old 03-15-2013, 07:12 AM   #2
asurarocks
Member
 
Location: Terre Haute, IN

Join Date: Nov 2010
Posts: 12
Default

If you are using MEDIPS package, INPUT sample is optional. I got decent numbers of DMRs without using input sample.
asurarocks is offline   Reply With Quote
Old 03-15-2013, 07:17 AM   #3
rachita
Junior Member
 
Location: Boston

Join Date: Mar 2013
Posts: 7
Default

Thanks for your reply.
rachita is offline   Reply With Quote
Old 09-03-2013, 01:47 AM   #4
mikep
Member
 
Location: Singapore

Join Date: Feb 2011
Posts: 45
Default

It appears it's not only optional, but actually ignored for the purpose of DMR analysis with the builtin edgeR

Why is that? Wouldn't some kind of input subtraction prior to differential analsyis be preferable?
mikep is offline   Reply With Quote
Old 04-20-2017, 04:38 AM   #5
tanaybhatt
Junior Member
 
Location: Bangalore

Join Date: Apr 2017
Posts: 3
Default

Can someone direct me to a published paper where DMR analysis has been done without taking the input in consideration (or without input subtraction/normalization)?
tanaybhatt is offline   Reply With Quote
Old 05-03-2017, 07:04 AM   #6
rachita
Junior Member
 
Location: Boston

Join Date: Mar 2013
Posts: 7
Default

Our data which was why the question was posted is not published. Here is the link "http://dx.doi.org/10.1080/21623945.2017.1320002". You can check that.

Last edited by rachita; 05-03-2017 at 07:22 AM.
rachita is offline   Reply With Quote
Old 05-03-2017, 07:21 AM   #7
asurarocks
Member
 
Location: Terre Haute, IN

Join Date: Nov 2010
Posts: 12
Default

Here you go:
http://journals.plos.org/plosone/art...l.pone.0147514
asurarocks is offline   Reply With Quote
Reply

Tags
input data, medip-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:52 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO