SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DEXSeq error in estimateDispersions: match.arg(start.method, c("log(y)", "mean")) fpadilla Bioinformatics 14 07-03-2013 03:11 PM
Relatively large proportion of "LOWDATA", "FAIL" of FPKM_status running cufflink ruben6um Bioinformatics 3 10-12-2011 01:39 AM
The position file formats ".clocs" and "_pos.txt"? Ist there any difference? elgor Illumina/Solexa 0 06-27-2011 08:55 AM
Normalization: DESeq vs. EdgeR with method="RLE" aquila RNA Sequencing 3 04-26-2011 10:00 AM
"Systems biology and administration" & "Genome generation: no engineering allowed" seb567 Bioinformatics 0 05-25-2010 01:19 PM

Reply
 
Thread Tools
Old 05-23-2013, 07:12 PM   #1
syintel87
Member
 
Location: Universe

Join Date: Dec 2012
Posts: 81
Default [EdgeR] exactTest dispersion="common"

While doing exactTest in EdgeR,
I can choose an option, dispersion= "common", "tagwise", or "auto".

My question is what is the difference between these two options. Which option is appropriate?

In my data analysis, common.dispersion 0.3064238.
If I did exactTest with dispersion="common", I've got p-values below.
Quote:
PValue (sorted from smallest to largest)
8.34E-08
1.23E-07
3.30E-07
3.81E-07
3.94E-07
4.72E-07
5.22E-07
5.27E-07
5.44E-07
However, if I did exactTest with dispersion="tagwise", I've got p-values below.
Quote:
PValue (sorted from smallest to largest)
0.00393925
0.003999847
0.004926992
0.005319714
0.005459274
0.005504967
0.005744749
0.005883501
0.005897807
These two results look quite different. Since I wanna use B&H (1995) method for p-value adjustment, if I choose common dispersion, I would gain a list of differentially expressed genes. However, if I choose tagwise dispersion, I would gain no gene which is differentially expressed.
Thank you in advance.
syintel87 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 07:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO