I'm trying to run Cuffdiff on a set of 10 human samples with biological
replication then download the results for further analyses in
Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get
cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff
output files to the names expected by cummerbund. Cummerbund builds a CuffSet
with no warnings and most analyses work as expected. The problem comes any
time I try to see the results of replication. For example, in cummerbund,
>replicates() returns an empty set and any type of plot returns an error when
replicates=T is included as an argument.
There is no evidence of replication data in any of the 11 cuffdiff output
files. The data is presented with the group name only. From this, I conclude
that the problem is with cuffdiff, since there is no replicate data for
cummerbund to build into its db. I see that there are several read group files
that are produced by cuffdiff but cannot be downloaded in Galaxy. Is this the
problem, and if so, how can Galaxy be used to generate data with (essential)
replication? Are the p and q significance values reported in the output
files a result of replicate analysis?
I have tried to ask this question in several different forums without success.
The responses I've gotten suggest its a Galaxy issue rather than either
cuffdiff or cummerbund. I'm hoping someone here can help answer my questions.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: