## User: bruce.moran

bruce.moran20
Reputation:
20
Status:
New User
Location:
Ireland
Last seen:
4 weeks, 1 day ago
Joined:
3 years, 10 months ago
Email:
b**********@gmail.com

#### Posts by bruce.moran

<prev • 15 results • page 1 of 2 • next >
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... Great, didn't think of it that way, thanks. ...
written 3 months ago by bruce.moran20
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... 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 3 months ago by bruce.moran20
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... 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 ...
written 3 months ago by bruce.moran20 • updated 3 months ago by Michael Love23k
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... 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 5 months ago by bruce.moran20
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... 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 5 months ago by bruce.moran20
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... 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         ...
written 5 months ago by bruce.moran20 • updated 5 months ago by Aaron Lun23k
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... 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 5 months ago by bruce.moran20
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... 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 ...
written 5 months ago by bruce.moran20
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... 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 ...
written 23 months ago by bruce.moran20 • updated 23 months ago by Julian Gehring1.3k
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... Thanks Florian, much appreciated! Bruce. ...
written 2.1 years ago by bruce.moran20

#### Latest awards to bruce.moran

Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq2 rlog error

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