User: jol.espinoz

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jol.espinoz10
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Posts by jol.espinoz

<prev • 25 results • page 1 of 3 • next >
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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 weeks ago by jol.espinoz10 • updated 22 days ago by Lluís R300
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Comment: C: RNA-Seq, generate batch-free count matrix
... Thank you for this! ...
written 4 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 6 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 6 months ago by jol.espinoz10 • updated 6 months ago by James W. MacDonald45k
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Comment: C: pvclust and distance matrices
... any luck with this ?  ...
written 9 months ago by jol.espinoz10
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... That was it. Thanks a lot Peter!   ...
written 9 months ago by jol.espinoz10
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Comment: C: WGCNA | Which module is reserved for outliers/unclustered genes?
... Perfect, thanks again Lluis!  I knew it was somewhere but I couldn't figure out which part of the docs to find it. Do you have any insight on https://support.bioconductor.org/p/91827/#91899 using a precomputed similarity measure as input? Peter gave some insight on the error and I'm wondering if the ...
written 9 months ago by jol.espinoz10
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... Yup, I think that was it.  So my SparCC correlation matrix has values out of range?  ...
written 9 months ago by jol.espinoz10
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... > max(abs(DF_mat - t(DF_mat)), na.rm = TRUE) [1] 1.000089e-12 ...
written 9 months ago by jol.espinoz10
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
... I wonder if it's b/c it's calling `checkAdjMat` instead of `checkSimilarity`?  ...
written 9 months ago by jol.espinoz10

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