User: jol.espinoz

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jol.espinoz20
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Posts by jol.espinoz

<prev • 33 results • page 1 of 4 • next >
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dynamicTreeCut and WGCNA show clusters overlapping. Why is this?
... 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 ...
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Comment: C: [metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormSt
... It's breaking here: `if (any(sapply(smat, length) == 1))    stop("Warning sample with one or zero features")` ...
written 6 months ago by jol.espinoz20
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
... 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 ...
metagenomeseq error cumnormstatfast features written 6 months ago by jol.espinoz20
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How to interpret WGCNA's modulePreservation output when comparing 2 networks?
... 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 ...
wgcna coexpression modules networks written 8 months ago by jol.espinoz20
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Answer: A: Cannot use Bioconductor with new conda R installation?
... 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 8 months ago by jol.espinoz20
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Cannot use Bioconductor with new conda R installation?
... 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:~ ...
biocinstaller installation bioconductor conda written 8 months ago by jol.espinoz20
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How to know which soft threshold to use for blockwise modules in WGCNA?
... 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 ...
wgcna coexpression transcriptome written 9 months ago by jol.espinoz20 • updated 9 months ago by Peter Langfelder1.6k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
... 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 ...
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Setting soft threshold when comparing 2 networks in WGCNA?
... 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 ...
network wgcna coexpression cooccurrence coabundance written 13 months ago by jol.espinoz20 • updated 12 months ago by Lluís Revilla Sancho430
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Comment: C: RNA-Seq, generate batch-free count matrix
... Thank you for this! ...
written 16 months ago by jol.espinoz20

Latest awards to jol.espinoz

Great Question 7 weeks ago, created a question with more than 5,000 views. For WGCNA: What is `soft thresholding`?
Popular Question 18 months ago, created a question with more than 1,000 views. For edgeR: How is FDR calculated for logFC? (False Discovery Rate)
Popular Question 18 months ago, created a question with more than 1,000 views. For WGCNA: What is `soft thresholding`?
Scholar 18 months ago, created an answer that has been accepted. For A: Cannot use Bioconductor with new conda R installation?

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