DESeq - working with more than 2 conditions
2
0
Entering edit mode
Natasha ▴ 440
@natasha-4640
Last seen 10.2 years ago
Dear Vincenzo, Unfortunately I don't think I can answer that. Perhaps others on the List could help. BW, Natasha From: Vincenzo Capece [mailto:vivo0304@gmail.com] Sent: 01 October 2012 09:04 To: Natasha Sahgal Subject: Re: [BioC] DESeq - working with more than 2 conditions Thanks a lot Natasha, edgeR is exactly what I was looking for. I am also a statistics beginner and I have an another question ,but I don't know if it's correct or not: To compute BCV in edgeR, why the developers didn't use ANOVA? I think that the MDS in edgeR is the same of SSB(sum of squares between) in ANOVA. Right? Thank you very much. On 13 September 2012 10:46, Natasha Sahgal <nsahgal@well.ox.ac.uk<mailto:nsahgal@well.ox.ac.uk>> wrote: Dear Vincenzo, You could try to use the edgeR package (and the glm method within it). Also, if I am not mistaken, you could use DESeq but you have to use the glm method there. Hope that helps, Natasha -----Original Message----- From: bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> [mailto:bioconductor- bounces@r-project.org<mailto:bioconductor-bounces@r-project.org>] On Behalf Of Vincenzo Capece Sent: 13 September 2012 07:53 To: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: [BioC] DESeq - working with more than 2 conditions Dear all, I am a R beginner and I hope you can help me. I have a question about DESeq: DESeq works fine if I have 2 conditions(treated,untreated) Example: treated untreated ENSMUSG00000000001 193 254 ENSMUSG00000000003 0 0 ENSMUSG00000000028 10 13 ENSMUSG00000000031 0 4 ENSMUSG00000000037 8 9 ENSMUSG00000000049 6 8 ... ... ... but if I have data about more than two conditions, for instance 1 -month-treated,3-months-treatead, 6-months-treated,untreated, can I use DESeq? If not, Which R package (if it exists)do you suggest to use? Thanks in advance. Regards. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Regards, Capece Vincenzo [[alternative HTML version deleted]]
edgeR DESeq edgeR DESeq • 1.6k views
ADD COMMENT
0
Entering edit mode
@vincenzo-capece-4556
Last seen 10.2 years ago
Thanks a lot Natasha, edgeR is exactly what I was looking for. I am also a statistics beginner and I have an another question ,but I don't know if it's correct or not: To compute BCV in edgeR, why the developers didn't use ANOVA? I think that the MDS in edgeR is s sort of SSB(sum of squares between) in ANOVA. Thank you very much. On 13 September 2012 10:46, Natasha Sahgal <nsahgal@well.ox.ac.uk> wrote: > Dear Vincenzo, > > You could try to use the edgeR package (and the glm method within it). > Also, if I am not mistaken, you could use DESeq but you have to use the > glm method there. > > > Hope that helps, > Natasha > > > -----Original Message----- > From: bioconductor-bounces@r-project.org [mailto: > bioconductor-bounces@r-project.org] On Behalf Of Vincenzo Capece > Sent: 13 September 2012 07:53 > To: bioconductor@r-project.org > Subject: [BioC] DESeq - working with more than 2 conditions > > Dear all, > I am a R beginner and I hope you can help me. > I have a question about DESeq: DESeq works fine if I have 2 > conditions(treated,untreated) > Example: > treated untreated > ENSMUSG00000000001 193 254 > ENSMUSG00000000003 0 0 > ENSMUSG00000000028 10 13 > ENSMUSG00000000031 0 4 > ENSMUSG00000000037 8 9 > ENSMUSG00000000049 6 8 > ... > ... > ... > > > but if I have data about more than two conditions, for instance > 1-month-treated,3-months-treatead, 6-months-treated,untreated, can I use > DESeq? If not, Which R package (if it exists)do you suggest to use? > > Thanks in advance. > Regards. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Regards, Capece Vincenzo [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
@thomas-j-hardcastle-3860
Last seen 7.1 years ago
United Kingdom
Dear Vincenzo, You may also want to take a look at the baySeq package, which handles multiple conditions in a different fashion to the glm approach of edgeR and DESeq - in some scenarios this is a better way to think about the data, in others, not. Tom
ADD COMMENT

Login before adding your answer.

Traffic: 838 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6