[BioC] 2 way anova in Bioconductor

[axel.klenk at actelion.com]

Hi Dana, 

ooops, obviously I shouldn't be posting immediately after lunch... 
re-reading
your message after some cups of coffee I realize that my brain has skipped
everything after male/female and treatment/control... so yours is clearly 
NOT
a 2x2 design... my apologies...

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
axel.klenk at actelion.com
To:
<Dana.Stanley at csiro.au>
Cc:
bioconductor at r-project.org, bioconductor-bounces at r-project.org
Date:
28.06.2011 15:13
Subject:
Re: [BioC] 2 way anova in Bioconductor
Sent by:
bioconductor-bounces at r-project.org



Hi Dana,

limma can do that easily. The current version of the user's guide
contains one chapter and two case studies on 2x2 factorial designs.

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland





From:
<Dana.Stanley at csiro.au>
To:
<bioconductor at r-project.org>
Date:
28.06.2011 03:27
Subject:
[BioC] 2 way anova in Bioconductor
Sent by:
bioconductor-bounces at r-project.org



Hi Everyone

I use custom designed chicken high-density multiplex one channel 
microarray (NimbleGen 12x135K). My usual pipeline includes mostly oligo, 
arrayQualityMetrics, preprocessCore, genefilter, GeneSelector and limma. 
So far I only worked with simple design, 2 conditions; control/treatment 
style. Now I have a dataset with embryonic development timeline for male 
and female chicks. I still compare different timepoints using limma but I 
want to do 2 way anova to identify interaction significant genes, ie genes 

where gender influences development timeline. I looked at many packages 
and could not find 2 way anova, though I am sure it is there somewhere. I 
tested package ABarray that seemed ideal for my me but after days of 
trying I contacted the author to find out that expression sets (mine is 
coming  from limma) can no longer be used by ABarray  as the package has 
not been updated for a while.  Can anyone suggest a package (and an 
example code if possible) for 2 way anova? I am so temp!
 ted to go and do it in GeneSpring...

Thanks all

Dana


                 [[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: 
http://news.gmane.org/gmane.science.biology.informatics.conductor




The information of this email and in any file transmitted with it is 
strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended 
recipient, any copying, distribution or any other use of this email is 
prohibited and may be unlawful. In such case, you should please notify the 
sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by 
letter.
Any views expressed in this message are those of the individual sender, 
except where the message states otherwise and the sender is authorised to 
state them to be the views of the sender's company. For further 
information about Actelion please see our website at 
http://www.actelion.com

_______________________________________________
Bioconductor mailing list
Bioconductor at r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: 
http://news.gmane.org/gmane.science.biology.informatics.conductor




The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by letter.
Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com