SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
discrepance in DESeq2 results with different design structures frymor Bioinformatics 1 04-30-2015 03:41 AM
samtools mpileup - different results for versions 0.19 x 1.1 clarissaboschi Bioinformatics 0 02-09-2015 10:37 AM
DESeq2 with no replicates - strange results frymor Bioinformatics 2 07-23-2014 02:17 AM
DESeq2 Results Error: Duplicate Rownames Not Allowed araschenbrenner Bioinformatics 4 06-26-2014 07:42 AM
The road after DESeq2 vs edgeR vs Cuffdiff results sindrle Bioinformatics 0 10-26-2013 01:34 AM

Reply
 
Thread Tools
Old 10-22-2015, 01:04 AM   #1
genomica
Junior Member
 
Location: United Kingdom

Join Date: Feb 2013
Posts: 9
Default Deseq2 results discrepancies because of versions of R

Hello all,

I was asked to repeat RNAseq analysis done a while ago. Previously, analysis was done using Deseq2 v1.2.10 and R v.3.0.2. Although we are still using the same version for Deseq2, R on our system is now upgraded to 3.2.1. Repeating exactly same analysis using the same code gives me half the number of genes as significantly expressed.

Does anyone know why this discrepancy could be?

Many thanks for any help you can provide.
genomica is offline   Reply With Quote
Old 10-22-2015, 02:16 AM   #2
genomica
Junior Member
 
Location: United Kingdom

Join Date: Feb 2013
Posts: 9
Default

Please ignore the previous post. It was my bad in noting the versions of Deseq2. Its v1.2.10 for R3.0.2 and v1.10 for R3.2.0. Sorry!
genomica is offline   Reply With Quote
Old 10-23-2015, 03:43 AM   #3
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

we discourage users from simultaneously cross posting, because it duplicates the effort of people trying to help

if your post is answered on another forum, you can help out other users and answer-ers by cross linking

https://support.bioconductor.org/p/73676/
Michael Love is offline   Reply With Quote
Old 10-23-2015, 04:31 AM   #4
genomica
Junior Member
 
Location: United Kingdom

Join Date: Feb 2013
Posts: 9
Default

Sorry about that, Michael. I will keep this in mind.
genomica 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 07:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO