SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Database of tumor-normal reads desmo Bioinformatics 2 03-27-2014 10:21 AM
Seurat - Analysis tool for tumor/normal DNA and RNA seq alexischr Bioinformatics 5 10-31-2013 10:16 AM
Available tumor-normal dataset with result (CNV, Snp and Indels) desmo Bioinformatics 1 01-21-2013 03:41 AM
UnifiedGenotyper between tumor and normal kasthuri Bioinformatics 3 07-21-2012 08:47 AM
Tumor/Normal comparison tool for VCF? NGSNewbie1 Bioinformatics 9 06-14-2012 08:46 PM

Reply
 
Thread Tools
Old 07-26-2013, 07:17 PM   #1
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default Is it possible to do DE analysis on single tumor-normal pair with EdgeR?

I heard that if you have multiple tumor-normal pairs, you can estimate the BCV. Then you can use this BCV to find DE genes for each individual tumor-normal pair.

Is this true? If so, how to use BCV to find DE genes for individual tumor-normal pairs. I couldn't find that in the EdgeR manual.

Thanks very much in advance!
ymc is offline   Reply With Quote
Old 07-27-2013, 01:28 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Regardless of the software you use, a 1 vs. 1 comparison will always yield close to useless results.
dpryan is offline   Reply With Quote
Old 07-27-2013, 05:15 PM   #3
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

Thanks for your reply.

I have another question. I currently have six pairs of lung tumor-normal pairs RNA-seq data. Suppose I later obtain another six pairs of breast tumor-control RNA-seq data. Can I mix them up for a combined analysis?

Can you tell me why this is not ok? It seems to me even for the "same" lung tumor, there might be heterogeneity among them. Therefore it appears to me "different" cancer can be mixed. Is that correct?
ymc is offline   Reply With Quote
Old 07-28-2013, 12:52 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

I suppose you could, if you're looking for commonalities between the tumors. It all depends on the biological question you want to ask.
dpryan is offline   Reply With Quote
Reply

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 04:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO