User: jol.espinoz

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jol.espinoz10
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Posts by jol.espinoz

<prev • 30 results • page 1 of 3 • next >
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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 6 weeks ago by jol.espinoz10
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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 weeks ago by jol.espinoz10
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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 weeks ago by jol.espinoz10
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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 weeks ago by jol.espinoz10 • updated 9 weeks ago by Peter Langfelder1.4k
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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 6 months ago by jol.espinoz10 • updated 5 months ago by Lluís R310
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Comment: C: RNA-Seq, generate batch-free count matrix
... Thank you for this! ...
written 9 months ago by jol.espinoz10
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Comment: C: Can edgeR TMM normalization be used for other count data?
... 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 12 months ago by jol.espinoz10
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Can edgeR TMM normalization be used for other count data?
... This question is split into 2 parts: (1) Can TMM normalization through edgeR be used for other count data like OTU counts and contig counts?  (2) After you calculate TMM, would converting to RPKM be more useful for looking at contig counts data since the range of lengths is pretty wide; if the abo ...
normalization edger counts tmm written 12 months ago by jol.espinoz10 • updated 12 months ago by James W. MacDonald46k
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Comment: C: pvclust and distance matrices
... any luck with this ?  ...
written 14 months ago by jol.espinoz10

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