Question: Cuffdiff-Cummerbund With Biological Replicates Problem
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Mike Shamblott • 20 wrote:
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.
Hopeful,
Mike
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modified 5.3 years ago
by
Jeremy Goecks • 2.2k
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written
5.3 years ago by
Mike Shamblott • 20
