User: charles.foster

Reputation:
20
Status:
New User
Location:
Last seen:
1 day, 20 hours ago
Joined:
9 months, 2 weeks ago
Email:
c*************@sydney.edu.au

Posts by charles.foster

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
39
views
1
answers
Comment: C: WGCNA sample size minimum: why?
... Great, thanks for the fast clarification! ...
written 1 day ago by charles.foster20
3
votes
1
answer
39
views
1
answer
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 2 days ago by charles.foster20 • updated 2 days ago by Peter Langfelder2.1k
1
vote
1
answer
132
views
1
answers
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 9 weeks ago by charles.foster20
2
votes
1
answer
132
views
1
answer
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 10 weeks ago by charles.foster20
1
vote
1
answer
111
views
1
answer
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 3 months ago by charles.foster20 • updated 12 weeks ago by Nadia Davidson280
1
vote
1
answer
102
views
1
answer
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 4 months ago by charles.foster20 • updated 4 months ago by Michael Love24k
0
votes
1
answer
316
views
1
answers
Comment: C: Interpreting the results from lfcShrink() with apeglm in DESeq2
... Hi Michael, Great- thanks for the clarification and great program! ...
written 9 months ago by charles.foster20
3
votes
1
answer
316
views
1
answer
Interpreting the results from lfcShrink() with apeglm in DESeq2
... Dear all, I'm relatively new to differential expression analysis of RNA-Seq data, and I'm working my way through the DESeq2 vignette to come to terms with how it works. I'm looking to obtain a set of genes with a log2 fold change >2, and an adjusted p-value of <0.001. Following the "standard" ...
deseq2 lfcshrink apeglm written 9 months ago by charles.foster20 • updated 9 months ago by Michael Love24k

Latest awards to charles.foster

Scholar 9 months ago, created an answer that has been accepted. For A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 137 users visited in the last hour