Question: systemPipeR with DESeq2
0
gravatar for Ugo Borello
5.1 years ago by
Ugo Borello340
France
Ugo Borello340 wrote:

Dear Thomas,

I was wondering if there is an easy way of using systemPipeR with DESeq2.

Thank you

 

Ugo

deseq2 systempiper • 808 views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Ugo Borello340
Answer: systemPipeR with DESeq2
0
gravatar for Thomas Girke
5.1 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:
Hi Ugo, Not right now but you can just run it as it is intended by DESeq2 and still make use of all the other functionalities in systemPipeR. The run_edgeR function is just a convenience wrapper function for edgeR which is limited to very simple pairwise experimental designs. If necessary I could add a similar one for DESeq2. Best, Thomas On Tue, Oct 21, 2014 at 02:24:12PM +0000, Ugo Borello [bioc] wrote: > Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> > > User Ugo Borello<https: support.bioconductor.org="" u="" 5753=""/> wrote Question: systemPipeR with DESeq2<https: support.bioconductor.org="" p="" 62160=""/>: > > Dear Thomas, > > I was wondering if there is an easy way of using systemPipeR with DESeq2. > > Thank you > > > > Ugo > > ________________________________ > > You may reply via email or visit systemPipeR with DESeq2
ADD COMMENTlink written 5.1 years ago by Thomas Girke1.7k
Answer: systemPipeR with DESeq2
0
gravatar for Ugo Borello
5.1 years ago by
Ugo Borello340
France
Ugo Borello340 wrote:

Thank you, Thomas, for your reply.

 

And what about the filterDEGs() function, could I use it with the results obtained with DESeq2 and then take advantage of the systemPipeR workflow for downstream GO analysis?

 

Ugo

ADD COMMENTlink written 5.1 years ago by Ugo Borello340
This would require the same naming structure of the column titles in the input data frame (degDF) to filterDEGs where the FDR column names are expected to end with "_FDR" and the log fold change columns with "_logFC". Perhaps try it out with the example with edgeR and then make sure your DESeq2 results are provided in the same format. Thomas On Tue, Oct 21, 2014 at 03:40:28PM +0000, Ugo Borello [bioc] wrote: > Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> > > User Ugo Borello<https: support.bioconductor.org="" u="" 5753=""/> wrote Answer: systemPipeR with DESeq2<https: support.bioconductor.org="" p="" 62160="" #62164="">: > > Thank you, Thomas, for your reply. > > > > And what about the filterDEGs() function, could I use it with the results obtained with DESeq2 and then take advantage of the systemPipeR workflow for downstream GO analysis? > > > > Ugo > > ________________________________ > > You may reply via email or visit A: systemPipeR with DESeq2
ADD REPLYlink written 5.1 years ago by Thomas Girke1.7k
Answer: systemPipeR with DESeq2
0
gravatar for Ugo Borello
5.1 years ago by
Ugo Borello340
France
Ugo Borello340 wrote:

I will try, thank you

Ugo

 

ADD COMMENTlink written 5.1 years ago by Ugo Borello340
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