Deseq2 results discrepancies because of versions of R

genomica · 10-22-2015, 01:04 AM

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 · 10-22-2015, 02:16 AM

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!

Michael Love · 10-23-2015, 03:43 AM

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/

genomica · 10-23-2015, 04:31 AM

Sorry about that, Michael. I will keep this in mind.

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10-22-2015, 01:04 AM	#1
genomica Junior Member Location: United Kingdom Join Date: Feb 2013 Posts: 9	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.

10-22-2015, 02:16 AM	#2
genomica Junior Member Location: United Kingdom Join Date: Feb 2013 Posts: 9	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!

10-23-2015, 03:43 AM	#3
Michael Love Senior Member Location: Boston Join Date: Jul 2013 Posts: 333	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/

10-23-2015, 04:31 AM	#4
genomica Junior Member Location: United Kingdom Join Date: Feb 2013 Posts: 9	Sorry about that, Michael. I will keep this in mind.