[BioC] CummeRbund multiple cases

Himanshu Sharma hsharm03 at students.poly.edu
Fri Jun 21 16:13:17 CEST 2013

Thanks a lot Loyal, 
I am trying to do a comparison of drug treatment on various resistant and sensitive tumors. I will think about how I can design the cuffdiff analysis to merge them all together. 
I really appreciate your effort to reply back.
From: Loyal A. Goff [lgoff at csail.mit.edu]
Sent: Friday, June 21, 2013 10:05 AM
To: Himanshu Sharma
Cc: bioconductor at r-project.org
Subject: Re: [BioC] CummeRbund multiple cases

Hi Himansu,
It is certainly possible to have 2-3 different concurrent connections to the different SQLite databases that would allow you to interact with all of the data points in the same session, but at this point, there is no seamless way to 'integrate' the results of multiple cuffdiff runs.  This is by design however as each cuffdiff run does its own model fitting and normalization that allows samples within a run to be directly comparable.  Depending on what it is you are trying to do, the best solution may be to create a new cuffdiff analysis that incorporates all samples across all analyses.  Please let me know if I can be of any more specific help.


On Jun 20, 2013, at 1:32 PM, Himanshu Sharma <hsharm03 at students.poly.edu> wrote:

> Dear Community,
> I have my RNA-seq Differential expression results from Cuffdiff. I would like to make some plots and figures using CummeRbund. I have been using it for quite sometime and find it really good. I wanted to ask if I could combine 2-3 different analyses and merge the results in Cummerbund?.
> Thanks,
> Himanshu
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