User: Peter Langfelder

gravatar for Peter Langfelder
Reputation:
1,520
Status:
Trusted
Location:
United States
Last seen:
1 week ago
Joined:
7 years, 7 months ago
Email:
p***************@gmail.com

Posts by Peter Langfelder

<prev • 247 results • page 2 of 25 • next >
0
votes
1
answers
151
views
1
answers
Comment: C: WGCNA: Understanding module-trait correlations
... The default in WGCNA is, for historical reasons, unsigned network (at least for most functions). You need to check the help file for each function you want to use; most functions where network type matters will have an argument networkType or just type. TOM type is not related to network type and o ...
written 7 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
151
views
1
answers
Comment: C: WGCNA: Understanding module-trait correlations
... You got it exactly right. I would only add that instead of running an unsigned analysis, I personally prefer to run a signed or signed hybrid, and then look at whether anti-correlated modules could be thought of as part of a single biological pathway/process. In my work, negatively correlated module ...
written 7 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
151
views
1
answers
Comment: C: WGCNA: Understanding module-trait correlations
... Apologies for the late reply. We recommend using a signed or signed hybrid network analysis. You can read some more here: http://www.peterlangfelder.com/signed-or-unsigned-which-network-type-is-preferable/ and http://www.peterlangfelder.com/two-types-of-signed-networks-in-wgcna/ Peter ...
written 8 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
151
views
1
answers
Comment: C: WGCNA: Understanding module-trait correlations
... There are two different correlations (or sets of correlations) that you need to distinguish. The eigengene-trait correlation measures the strength and direction of association between the module (more precisely, the representative profile) and the trait. If this is positive (negative), it means the ...
written 8 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
151
views
1
answers
Answer: A: WGCNA: Understanding module-trait correlations
... Your question is not very clear but I'll try anyway. The module-trait heatmap usually represents the correlations of the module eigengenes with traits. When that correlation is high, it means the eigengene increases with increasing trait. In a signed network (where all genes in a module are positive ...
written 8 weeks ago by Peter Langfelder1.5k
0
votes
3
answers
1.2k
views
3
answers
Comment: C: How to create "trait data" file for WGCNA
... It depends on what question you want to ask. Do you want to see modules that relate to each treatment group vs. controls? Then create one variable for each treatment group. Call the variables groupVar1, groupVar2, groupVar4, groupVar8. Define the groupVar1 [2,4,8] variable to be 1 if the sample is t ...
written 10 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
106
views
1
answers
Comment: C: problem for Using RNA-seq data-set in WGCNA
... Change the line probes2annot = match(probes,GeneAnnotation$substanceBXH) to probes2annot = match(probes,GeneAnnotation$gene_id)   You may also want to change ProbeID=names(datExprFemale), GeneAnnotation[probes2annot,] to just GeneAnnotation[probes2annot, c("gene_id", "gene_name")] and you ...
written 12 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
174
views
1
answers
Comment: C: WARNING: remove set.seed usage in R code
... You're right, I didn't think of the possibility of calling code defining its own .Random.seed (which is probably not very frequent but certainly possible). ...
written 12 weeks ago by Peter Langfelder1.5k
0
votes
1
answers
106
views
1
answers
Answer: A: problem for Using RNA-seq data-set in WGCNA
... It depends what your RNA seq data is summarized to. If it summarized to genes, you don't necessarily need any probe to gene mapping, that is, you can drop all parts of code referring to GeneAnnotation. As an aside, I (and my collaborators) like to have some basic information about the genes (e.g., ...
written 3 months ago by Peter Langfelder1.5k
0
votes
1
answers
174
views
1
answers
Comment: C: WARNING: remove set.seed usage in R code
... The proper way would be to test whether .Random.seed exists, save and restore it upon exit. In my packages (which live on CRAN, not Bioconductor) I also tend to allow the user to request that the random seed not be set within the function, by supplying NULL to the argument randomSeed below. foo = ...
written 3 months ago by Peter Langfelder1.5k

Latest awards to Peter Langfelder

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Guru 4 months ago, received more than 100 upvotes.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
Scholar 15 months ago, created an answer that has been accepted. For A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA - soft threshold
Scholar 15 months ago, created an answer that has been accepted. For A: How to know which soft threshold to use for blockwise modules in WGCNA?
Scholar 15 months ago, created an answer that has been accepted. For A: novice: building gene co-expression network using RNA-Seq data
Scholar 15 months ago, created an answer that has been accepted. For A: How to get an output from DESeq2 to be used in WGCNA package
Scholar 20 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 2.6 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 2.8 years ago, created 100 posts.
Scholar 2.9 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 281 users visited in the last hour