SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GC bias correction Robby Bioinformatics 0 07-18-2011 07:38 AM
bug in memory allocation in cuffdiff with bias correction biterbilen Bioinformatics 0 06-03-2011 09:18 AM
Length bias correction for biological replicates pinki999 Bioinformatics 0 02-24-2011 11:37 PM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses. Newsbot! Literature Watch 0 01-22-2011 02:02 AM
transcript length bias in enrichment analysis and RPKM PFS RNA Sequencing 1 12-12-2010 05:32 PM

Reply
 
Thread Tools
Old 01-21-2014, 08:41 AM   #1
lukas1848
Member
 
Location: Germany

Join Date: Jun 2011
Posts: 54
Smile RNAseq, GO enrichment, and length bias correction

Hi,

I have a set of DE genes from an RNAseq study in a non-model species. I performed a GO enrichment analyses using topGO and GOseq.
TopGO is nice, because it offers the parent-child algorithm, which takes into account the hierachical relationship between GOs. GOseq is nice, because it corrects for length bias in RNAseq.
Yet, of course I would like to combine both advantages. Ideally, I would just run topGO and perform a length bias correction on the calculated p values.
I found a paper by Gao et al. (http://bioinformatics.oxfordjournals.../27/5/662.long), where they essentially describe how to do this, at least that is what I understood, but to be fair, I am neither a bioinformatician nor a statistician.
The problem is, the R scripts mentioned in the paper are no longer available.

So my question is: Is there a simple way to correct for the RNAseq length bias, by just correcting the p values returned by topGO's fisher tests? I imagine to just multiply the p values by a correction factor based on the average transcript length in the respective GO term.

I hope some of you might have an idea on that.

Thanks,

Lukas

Last edited by lukas1848; 01-21-2014 at 08:44 AM.
lukas1848 is offline   Reply With Quote
Old 01-21-2014, 09:03 AM   #2
chadn737
Senior Member
 
Location: US

Join Date: Jan 2009
Posts: 392
Default

Did you try emailing the authors about the scripts?
chadn737 is offline   Reply With Quote
Old 01-21-2014, 10:29 AM   #3
lukas1848
Member
 
Location: Germany

Join Date: Jun 2011
Posts: 54
Default

yes, I did. The author will try to fix the link. But I am not sure that I will find a simple answer to my question in the script.
lukas1848 is offline   Reply With Quote
Old 01-22-2014, 04:13 AM   #4
lukas1848
Member
 
Location: Germany

Join Date: Jun 2011
Posts: 54
Default

Quote:
Originally Posted by lukas1848 View Post
yes, I did. The author will try to fix the link. But I am not sure that I will find a simple answer to my question in the script.
Ok. I got the scripts, but they didn't really help me in answering my question.

Edit: I got another answer from the author and unfortunately, it's not as simple as I hoped. I have to estimate the noncentral parameter for the Wallenius distribution based on transcript length before I calculate my p values. This won't be easy to implement into my topGO workflow. Is anyone here aware of a program that can do both, lenght bias correction and parent-child testing for GO enrichments?

Last edited by lukas1848; 01-22-2014 at 06:47 AM.
lukas1848 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 11:08 AM.


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