Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe28k
Reputation:
27,980
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Trusted
Location:
USA / Europe / Brazil
Website:
https://github.com/kev...
Last seen:
4 hours ago
Joined:
1 year ago
Email:
k**********@outlook.com

From Republic of Ireland. Currently Consultant Bioinformatician and Visiting Professor in Clinical Bioinformatics.

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Developer / Maintainer of Bioconductor packages:

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There are mountains in our way... but we climb a step every day...

Dreams are hard to follow, but don't let anyone tear them away...  A hero lies in you...

Nella fantasia, io vedo un mondo giusto; Lì, tutti vivono in pace e in onestà; Io sogno d'anime che sono sempre libere...

Posts by Kevin Blighe

<prev • 4,205 results • page 2 of 421 • next >
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Answer: A: connecting proteins with SNPS using cell lines
... It is 'possible', indeed; however, it is better to obtain 'real' samples and to avoid the use of cell-lines. Kevin ...
written 18 hours ago by Kevin Blighe28k
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Answer: A: Antibody microarray data to construct co-expression network
... It is not the greatest dataset for this purpose. In each cell-line, you have just a 1 versus 1 comparison. You cannot faithfully construct a co-expression network from just 1 or 2 samples. An alternative would be to create separate networks for all controls (n=5) and all treated (n=5); however, eve ...
written 18 hours ago by Kevin Blighe28k
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Comment: C: CNV and pseudogenes
... Even if you did exclude the region for the analysis, how could you even be sure that the original reads themselves did not derive [in part] from the pseudogene. Unfortunately, some regions of the genome are impossible to be faithfully analysed by ***short read*** NGS technology. If your group is st ...
written 18 hours ago by Kevin Blighe28k
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Comment: C: Eigen genes using WGCNA
... ...but, *black* is just *MEblack*, *grey* is *MEgrey*, et cetera. An eigen-gene is an abstraction of a gene - the eigen-gene values are unit-less and are derived via PCA. Conversely, a module is an abstraction of an eigenvector. ...
written 1 day ago by Kevin Blighe28k
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Answer: A: Display pairwise p values on barplots in ggplot2
... That guy just pulled that plot from this tutorial, where it explains how to do it: Add P-values and Significance Levels to ggplots ----------------------------------- ---------- Another way is to do it manually via `geom_segment()` and `geom_text()`, as I did here: https://www.biostars.org/p/30686 ...
written 1 day ago by Kevin Blighe28k
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Comment: C: WGCNA: Output gene lists from consensus network modules
... Tutorial now moved to: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ Kevin ...
written 1 day ago by Kevin Blighe28k
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Answer: A: Eigen genes using WGCNA
... I have looked up previous WGCNA code that I used (when I was actually working in the lab where the method was developed) and you should be able to produce the gene-to-eigengene colour assignments via: data.frame(colnames(datExpr), mergedColors) Kevin ...
written 1 day ago by Kevin Blighe28k
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Comment: C: Eigen genes using WGCNA
... Please don't post another question as an answer. We will get around to it when we have time. We are volunteers here, each with our own full-time job (or jobs) and struggles that we face. ...
written 1 day ago by Kevin Blighe28k
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... Cross-posted on Bioconductor: https://support.bioconductor.org/p/113105/ ...
written 1 day ago by Kevin Blighe28k
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Comment: C: problem with facing strange gene name in TCGA data
... Most of them likely have had official gene symbols assigned since the TCGA project. You can look up each of them and assign them their new name. ...
written 1 day ago by Kevin Blighe28k

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