User: Dave Wettmann
Dave Wettmann • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- United Kingdom
- Last seen:
- 2 years, 9 months ago
- Joined:
- 5 years ago
- Email:
- d*************@gmail.com
Posts by Dave Wettmann
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... Hello,
I'm looking at objects generated using the previous version of SomaticSignatures in the latest version. The objects were generated as part of the example in the vignette but they now seem to produce errors when I try to plot them e.g.
> plotSampleMap(sigs_nmf)
Error in (function (clas ...
written 4.7 years ago by
Dave Wettmann • 40
• updated
4.7 years ago by
James W. MacDonald ♦ 50k
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... I've just updated to v2 along with BioC v3 and thought this is a superb package. I would like to analyse my data using the new "21 signatures" data but could you confirm the only way of doing so is using them as described by Muller in his original question please?
Best,
Dave
...
written 4.7 years ago by
Dave Wettmann • 40
0
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Comment:
C: No significant p-values
... Thanks Lucia; I've checked that PCs 1 and 2 capture 55% and 15% of the
total variance, respectively. Could you explain how, if I did find
that
the treatment effect was present in another PC, that would help me
please?
I don't have any positive control because it's an experiment to
characterise a r ...
written 5.0 years ago by
Dave Wettmann • 40
0
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Comment:
C: No significant p-values
... Thanks Mike - yes I used the sensitive vs resistant contrast argument
to
results()
On 27 June 2014 14:39, Michael Love
wrote:
> hi Dave,
>
> If you don't find a set of genes with low FDR, then the experiment
could
> have been underpowered to find the small differences, i.e. not
enoug ...
written 5.0 years ago by
Dave Wettmann • 40
0
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510
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Comment:
C: DESeq analysis of resistance data
... Hi Mike,
Thanks for your reply; my interest would be in the genes that are
differentially expressed in the resistant cells versus the sensitive
cells
but also using the control samples to identify any differentially
expressed
genes which changing as a result of a "non-specific" effect of
treatment
...
written 5.0 years ago by
Dave Wettmann • 40
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