User: jol.espinoz
jol.espinoz • 10
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Posts by jol.espinoz
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... It's breaking here: `if (any(sapply(smat, length) == 1))
stop("Warning sample with one or zero features")`
...
written 4 months ago by
jol.espinoz • 10
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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 4 months ago by
jol.espinoz • 10
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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 6 months ago by
jol.espinoz • 10
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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
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written 7 months ago by
jol.espinoz • 10
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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 7 months ago by
jol.espinoz • 10
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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 7 months ago by
jol.espinoz • 10
• updated 7 months ago by
Peter Langfelder • 1.5k
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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 7 months ago by
jol.espinoz • 10
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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 11 months ago by
jol.espinoz • 10
• updated 11 months ago by
Lluís R • 370
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... Thank you for this!
...
written 14 months ago by
jol.espinoz • 10
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... These answers are great. Thank you James & Aaron. So could it be simplified to the idea that TMM normalization can be used if the counts from one attribute influence the counts for another attribute and if most of the attributes should not be dramatically different between samples? For example ...
written 17 months ago by
jol.espinoz • 10
Latest awards to jol.espinoz
Popular Question
17 months ago,
created a question with more than 1,000 views.
For source(biocLite.R) leads to this error >>> Peer certificate cannot be authenticated with given CA certificates
Popular Question
17 months ago,
created a question with more than 1,000 views.
For edgeR: How is FDR calculated for logFC? (False Discovery Rate)
Popular Question
17 months ago,
created a question with more than 1,000 views.
For WGCNA: What is `soft thresholding`?
Scholar
17 months ago,
created an answer that has been accepted.
For A: Cannot use Bioconductor with new conda R installation?
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