User: jol.espinoz
jol.espinoz • 20
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Posts by jol.espinoz
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... Can somebody explain why I am seeing certain clusters overlap? I tried reproducing the results in Python and in R and I'm seeing a similar pattern.
I have 2 main questions:
(1) Do the colors from WGCNA get repeated? It looks like the 2nd red cluster from the left should be a different color based ...
written 7 months ago by
jol.espinoz • 20
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... It's breaking here: `if (any(sapply(smat, length) == 1))
stop("Warning sample with one or zero features")`
...
written 12 months ago by
jol.espinoz • 20
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... I'm trying to follow a slight variant of the tutorial to get started from ~ page 9: https://www.bioconductor.org/packages/devel/bioc/vignettes/metagenomeSeq/inst/doc/metagenomeSeq.pdf
Essentially, I need to figure out how to go from: (A) my raw Otu counts; and (B) my "class" assignment (e.g. diseas ...
written 12 months ago by
jol.espinoz • 20
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... I'm trying to compare 2 networks that I've created as a toy dataset from WGCNA's tutorial section I'm not exactly sure how to interpret the resulting data since there is so much content. X_A and X_B are adjacency matrices while modules_A and modules_B are the module assignments (starting at 0 and as ...
written 14 months ago by
jol.espinoz • 20
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These solved my problem. Definitely the second one and possibly the commented out one too.
#conda install gfortran_osx-64 --yes
conda install -c anaconda clangxx_osx-64 --yes
...
written 15 months ago by
jol.espinoz • 20
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... I'm having a lot of trouble trying to install WGCNA, edgeR, and limma. First I tried to just the base bioconductor packges but there was the following error:
conda create -n r_test python=3 --yes
conda activate r_test
conda install -c r r --yes
# This was successful
(r_test) jespinozlt-osx:~ ...
written 15 months ago by
jol.espinoz • 20
2
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... I want to try blockwise modules for WGCNA but I think I'm missing some points in logic.
If you have a dataset too large to run WGCNA (e.g. 100k genes) and want to run blockwise modules, how do you know which soft threshold to use to get a good scalefree topology for each of the networks?
I ...
written 15 months ago by
jol.espinoz • 20
• updated
15 months ago by
Peter Langfelder • 1.9k
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... I recently acquired a metatranscriptomics dataset. There are ~1 million ORFs and after strict filtering could be reduced to ~100 thousand ORFs. The dataset has treatment (N=49) and control (N=34) groups for a total of 83 samples.
I have access to compute resources which I can use for WGCNA.
I on ...
written 15 months ago by
jol.espinoz • 20
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309
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... I am using WGCNA to compare 2 networks of a healthy and a diseased state. I'm using the TOM matrix as a similarity measure and creating 2 fully connected networks (healthy and diseased). The healthy network has the highest scale-free topology using a power(beta) of 4 while the diseased network has ...
written 19 months ago by
jol.espinoz • 20
• updated
19 months ago by
Lluís Revilla Sancho • 470
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... Thank you for this!
...
written 22 months ago by
jol.espinoz • 20
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For WGCNA: What is `soft thresholding`?
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For source(biocLite.R) leads to this error >>> Peer certificate cannot be authenticated with given CA certificates
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For edgeR: How is FDR calculated for logFC? (False Discovery Rate)
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