User: bruce.moran

gravatar for bruce.moran
bruce.moran20
Reputation:
20
Status:
New User
Location:
Ireland
Last seen:
2 months, 4 weeks ago
Joined:
4 years, 4 months ago
Email:
b**********@gmail.com

Posts by bruce.moran

<prev • 15 results • page 1 of 2 • next >
0
votes
1
answer
240
views
1
answers
Comment: C: varianceStabilizingTransformation for clustering, deconvolution
... Great, didn't think of it that way, thanks. ...
written 10 months ago by bruce.moran20
0
votes
1
answer
240
views
1
answers
Comment: C: varianceStabilizingTransformation for clustering, deconvolution
... Yes, sorry I keep referring to VST as normalisation when it is a transformation. Your reply does address the central issue, of global dispersion and it's affect on the transformation. What I really want to get is an opinion as to which is 'more appropriate': 1. create a single `dds` object whic ...
written 10 months ago by bruce.moran20
0
votes
1
answer
240
views
1
answer
varianceStabilizingTransformation for clustering, deconvolution
... Hi, I have been using `varianceStabilizingTransformation()` for normailsation of gene expression data to allow use in deconvolution and clustering methods. However, having looked more closely I now see that splitting samples based on grouping (e.g. tissue type, or other phenotypic classification) a ...
normalization limma deseq2 deconvolution written 10 months ago by bruce.moran20 • updated 10 months ago by Michael Love26k
0
votes
1
answer
312
views
1
answers
Comment: C: Limma Voom duplicateCorrelation Design
... OK, good to know, and yes, with strong effect (tumour vs. normal) we find an effect as expected, but the diet effect is minimal. Not sure I won't worry about it though=D Thanks for your advice, and your continued support of these kinds of questions, it is incredibly helpful. ...
written 12 months ago by bruce.moran20
0
votes
1
answer
312
views
1
answers
Comment: C: Limma Voom duplicateCorrelation Design
... Hi Aaron, thanks for the reply, late response as I got no notification mail. I find very small change after second round of duplicateCorrelation: DTcor <- duplicateCorrelation(DTdcv, block=conds$Individual) DTcor$consensus.correlation [1] 0.4353269 DTdcv2 <- voom(DTdge, DTdesign, correlat ...
written 12 months ago by bruce.moran20
3
votes
1
answer
312
views
1
answer
Limma Voom duplicateCorrelation Design
... Hi, want to get this straight as my first time using limma-voom and duplicateCorrelation. My metadata has multiple Tissue (either tumour or normal) across two Diets. Each Individual had multiple biopsies, from either normal, tumour or multiple of each. conds     Individual Tissue Diet S1         ...
limma duplicatecorrelation voom written 12 months ago by bruce.moran20 • updated 12 months ago by Aaron Lun25k
0
votes
1
answer
255
views
1
answers
Comment: C: DESeq2 Design with Multiple Replicates of Individuals including Tumour and Norma
... Hi Michael, I RTFM'd again and came across the section you link, had remembered this but thought I would not be able to use as I do not have Normal and Tumour in all Individual. The edit I made above runs without error, which I did not think would be the case. However, this is not accounting for va ...
written 12 months ago by bruce.moran20
0
votes
1
answer
255
views
1
answer
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
... Hi, I have a bit of experience with simpler model designs in DESeq2. This is a slightly more complex design than usual so wanted to check how I might run the analysis. I have 35 samples from rats fed normal chow (NC) or high fat diet (HFD). These animals are bred to be susceptible to tumours. They ...
deseq2 design and contrast matrix written 12 months ago by bruce.moran20
0
votes
1
answer
413
views
1
answer
plotMutationSpectrum Colour By Patient with Multiple Samples
... Hi, I have multiple timepoint samples pre- and post-treatment for several patients. I cannot see a standard way to colour mutation spectrum by a 'group' variable, as opposed to sample or mutation. I have the group in the VRanges object supplied to mutationContext, but cannot force via scale_fill_br ...
somaticsignatures somaticsignatures package plotmutationspectrum written 2.4 years ago by bruce.moran20 • updated 2.4 years ago by Julian Gehring1.3k
0
votes
1
answer
965
views
1
answers
Comment: C: Gviz AnnotationTrack id above feature
... Thanks Florian, much appreciated! Bruce. ...
written 2.7 years ago by bruce.moran20

Latest awards to bruce.moran

Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 rlog error

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 380 users visited in the last hour