User: charles.foster

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Posts by charles.foster

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Subset WGCNA results for export to Cytoscape
... Hi Peter, Thanks for the reply. The green module lay between two different blocks, so I couldn't just load one block as suggested. I'll keep that in mind for future, though. I calculated the TOM just for the module genes, as Andres suggested. This was successful, and I have the necessary files fo ...
written 5 weeks ago by charles.foster40
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Comment: C: Subset WGCNA results for export to Cytoscape
... Hi again Andres, Thanks for the suggestion. I ran your code and it appeared to work, but the edges etc all had 'NA'. I think the subsetting of datExpr was wrong. I changed it to: ``` datexpr_green = datExpr[,moduleColors == module] ``` so that only the columns (not rows) were subset based on the g ...
written 5 weeks ago by charles.foster40
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Comment: C: Subset WGCNA results for export to Cytoscape
... Hi Andres, Thanks for the reply. The results are: ``` > class(TOM) [1] "dist" > dim(TOM) NULL > length(TOM) [1] 80182116 > dim(datExpr) [1] 12 41047 ``` The original command to generate the TOM was: ```net = blockwiseModules(datExpr, maxBlockSize = 20000, power = 18, networkType=" ...
written 6 weeks ago by charles.foster40
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Subset WGCNA results for export to Cytoscape
... Hi all, I am trying to export my results from WGCNA for network visualisation with visANT or Cytoscape. This step requires the topological overlap matrix (TOM) to be subset. Tutorial 6 on the WGCNA page deals with this: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tuto ...
wgcna written 6 weeks ago by charles.foster40 • updated 5 weeks ago by Peter Langfelder2.3k
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Comment: C: WGCNA sample size minimum: why?
... Great, thanks for the fast clarification! ...
written 3 months ago by charles.foster40
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WGCNA sample size minimum: why?
... Hi all, While looking into WGCNA analysis, I saw that the minimum recommended sample size is 15 samples because: > correlations on fewer than 15 samples will simply be too noisy for the network to be biologically meaningful I'm wondering if anyone here would be able to further clarify why this ...
wgcna written 3 months ago by charles.foster40 • updated 3 months ago by Peter Langfelder2.3k
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Answer: A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
... In case anyone is wondering in the future, I managed to solve the problem. The solution is a bit fiddly, but at least it works. First, load the clusterProfiler package, then read in your GOSeq enrichment results into a new data frame (in this case it's called ```results_df```). You need to format t ...
written 6 months ago by charles.foster40
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Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
... Hi all, I'm a big fan of the many plots produced by the clusterProfiler and enrichplot packages. The functions such as ```emapplot()``` require the enrichment results to have been generated using clusterProfiler (and a few other related packages, I think). However, I've carried out GO/KEGG enrichm ...
clusterprofiler enrichplot written 6 months ago by charles.foster40
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GOseq analysis with only upregulated or downregulated genes
... Dear all, I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq. I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths ...
goseq written 7 months ago by charles.foster40 • updated 6 months ago by Nadia Davidson300
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Finding genes that are expressed only in one condition within a contrast
... Hi, I have carried out differential expression analyses comparing conditions using DESeq2. Intuitively, I have considered genes to be expressed if they have a count of at least 10 in at least some libraries (sensu Chen et al: https://f1000research.com/articles/5-1438). Hence, I carried out a filter ...
deseq2 filter written 8 months ago by charles.foster40 • updated 8 months ago by Michael Love26k

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Scholar 13 months ago, created an answer that has been accepted. For A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res

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