User: Dave Wettmann

gravatar for Dave Wettmann
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
2 years, 1 month ago
Joined:
4 years, 4 months ago
Email:
d*************@gmail.com

Posts by Dave Wettmann

<prev • 5 results • page 1 of 1 • next >
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SomaticSignatures objects in new version
... 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 ...
somaticsignatures written 4.0 years ago by Dave Wettmann40 • updated 4.0 years ago by James W. MacDonald48k
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Comment: C: SomaticSignatures: Compare my datas with validated mutational signatures
... 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 4.0 years ago by Dave Wettmann40
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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 4.3 years ago by Dave Wettmann40
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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 4.3 years ago by Dave Wettmann40
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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 4.4 years ago by Dave Wettmann40

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