User: chrisclarkson100

Reputation:
30
Status:
New User
Location:
Last seen:
4 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
c***************@yahoo.co.uk

Posts by chrisclarkson100

<prev • 20 results • page 2 of 2 • next >
1
vote
1
answer
1.5k
views
1
answer
WGCNA configured network of low scale-free topology fit
...   I have visually assessed a number of networks configured by WGCNA. The one that I am most happy with however only has a scale-free topology fit of 0.6 R^2. As follows: My downstream analysis of this is to correlate external trait-info to this network: how sure can I be of any inferred correla ...
wgcna written 3.1 years ago by chrisclarkson10030 • updated 3.1 years ago by Peter Langfelder2.2k
0
votes
0
answers
449
views
0
answers
displaying network from microbial count data
... I have an abundance table of taxa (columns) and communities (rows). community acanthamoeba acetitomaculum acetivibrio acholeplasma achromobacter 1 AE01 0 0 0 0 1 2 AE02 0 0 0 0 ...
phyloseq written 3.2 years ago by chrisclarkson10030
0
votes
3
answers
3.5k
views
3
answers
Comment: C: voom for spectral counts
... Here is a related question relating to count data of microbial communities https://support.bioconductor.org/p/85552/ ...
written 3.2 years ago by chrisclarkson10030
2
votes
1
answer
701
views
1
answer
converting extremely sparse count dataframe to continuous distributions for study in WGCNA
... I am very inexperienced with mathematics and expression data. I have developed a pipeline for WGCNA, practicing with gene-expression microarray data. I am now determined to try to apply this strategy to microbial-communities count data.  Initially I tried finding an adjacency matrix with the natur ...
voom counts limma voom written 3.2 years ago by chrisclarkson10030 • updated 3.2 years ago by Gordon Smyth38k
0
votes
0
answers
839
views
0
answers
showing clusters in neworkd3 from WGCNA data
... I have successfully managed to plot an adjacency matrix graph in both igraph and networkD3. The display that I would like is for the WGCNA configured clustering-modules to show in both graphs. As of yet I have only managed to do this in igraph with the following code: library('igraph') library('ne ...
clustering networkd3 labels written 3.2 years ago by chrisclarkson10030
0
votes
2
answers
958
views
2
answers
Comment: C: most efficient way to read adjacency matrix to make networkd3 graph
... Thanks so much it seems to work like you said   ...
written 3.2 years ago by chrisclarkson10030
0
votes
2
answers
958
views
2
answers
Comment: C: most efficient way to read adjacency matrix to make networkd3 graph
... Hi yes I have checked with my own code and unfortunately, while the output is improved as the self-interactive nodes are no longer a problem (i.e. the nodes have correlation values for nodes besides themselves), the output is till different to that of the 'for loop' code- self-interating means that ...
written 3.2 years ago by chrisclarkson10030
0
votes
2
answers
958
views
2
answers
Comment: C: most efficient way to read adjacency matrix to make networkd3 graph
... Hi there thanks for the reply, while your code gets rid of the problem with needing to specify "arr.ind=TRUE" it produces the same output as the unwanted df given above- where it only seems to take self -interacting nodes into account.... do you reckon there is something wrong with the 'for loop' co ...
written 3.2 years ago by chrisclarkson10030
0
votes
2
answers
958
views
2
answers
Comment: C: most efficient way to read adjacency matrix to make networkd3 graph
... hi there, thanks for the reply does this adj matrix work for you?            6450255     2570615      6370619       2600039     2650615      5340672       2000519     3870044 6450255  1.0000000  0.27049207 -0.189722700  0.4304964296  0.26144185  0.203182365  0.5261722409  0.28750105 2570615  0.2704 ...
written 3.2 years ago by chrisclarkson10030
1
vote
2
answers
958
views
2
answers
most efficient way to read adjacency matrix to make networkd3 graph
... I am inexperienced with iteration in R and am hoping to speed up a process as I am implementing some analysis in a website. I realise this may be a Q for Stackoverflow but I couldn't get an answer from them.. I found a very useful tutorial that allows me to iterate through an adjacency matrix (used ...
R iterators performance written 3.2 years ago by chrisclarkson10030 • updated 3.2 years ago by phil.chapman140

Latest awards to chrisclarkson100

Popular Question 15 months ago, created a question with more than 1,000 views. For WGCNA configured network of low scale-free topology fit

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 255 users visited in the last hour