User: catagui

gravatar for catagui
catagui30
Reputation:
30
Status:
New User
Location:
Miami, FL, USA
Last seen:
3 weeks, 6 days ago
Joined:
4 years, 11 months ago
Email:
c******@gmail.com

Postdoctoral Researcher, CIMAS/NOAA-AOML

Posts by catagui

<prev • 28 results • page 1 of 3 • next >
1
vote
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... Hi Kevin thanks for all the advice. I learned a lot of different ways to input data into wgcna. I will make sure to explain this in the methods and hopefully I will get some useful data. You don't like WGCNA? ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... When I to CPM the counts in edgeR then again it doesn't reach 0.9, tried different prior.count as below. So by using the 'calcNormFactors' I am normalizing the libraries, but I also need to normalize all the counts to e.g. log? Then if I just use the 'calcNormFactors' and input these values to WGC ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... I tried a couple of numbers but even 100 would not reach the 0.9 as the first figure below. Then I tried edgeR with the TMM matrix and was able to get to 0.9, however I am not sure if this is correct since I didn't transform the data and the boxplot shows all the samples at 0. counts <-read ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... The reason why I want to use wgcna is to compare it with the host data. These reads are from the algae that lives in symbiosis with the coral. When I analyzed the coral data I got really nice results, since I was able to get the gene modules that response to treatment and ones that are specific for ...
written 5 weeks ago by catagui30
0
votes
1
answer
6.5k
views
1
answers
Comment: C: Network plot from expression data in R using igraph
... Hi Kevin, If I understand this correctly. I take my counts data and normalize it first e.g use rlog of the counts. Then I need to find the genes that have a significant effect as the code below. However, I am bit confuse of what I should input in where is says: "y ~ estrogen *time.h" . Is this mean ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... I agree it is difficult. I can see how the pca shows what I get with differential gene expr. analyses. Were all the response happens at T2 except for geno C that also has a response at T1. This is a heat stress treatment, two time points. Maybe I should try to get rid of the ones whose mean is abo ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... Hi Kevin, Thanks for the help with this. Below are the rlog boxplot and dispersion plot. I just tried to input the TMM normalized matrix (got it from RSEM), also filtered as you suggested but still get those negative values (plot below). I will have a look at the paper, and see if edgeR can help. ...
written 5 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... I get the same 0 biased. Not sure if I am explaining properly, but they both have the same number of gene/isoform Ids since I decided leave the longer isoform per gene in my transcriptome. ![gene_counts histogram][1] [1]: https://i.ibb.co/F66VgpH/histogram-genecounts.jpg ...
written 6 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... When I tried to run the "estimateSizeFactors" I was getting the error below then follow the geoMeans solution I have above. “Error in estimateSizeFactorsForMatrix(counts(object), locfunc, geoMeans = geoMeans) : every gene contains at least one zero, cannot compute log geometric means”. But I am ...
written 6 weeks ago by catagui30
0
votes
0
answers
317
views
0
answers
Comment: C: WGCNA soft thresholding problem
... You are right it is bimodal. ![rlog histogram][1] [1]: https://i.ibb.co/fvCkDQF/histogram.jpg ...
written 6 weeks ago by catagui30

Latest awards to catagui

Great Question 8 months ago, created a question with more than 5,000 views. For Options for generating proportional Venn Diagram of 4 sets
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Options for generating proportional Venn Diagram of 4 sets

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1617 users visited in the last hour