Questions tagged [wgcna]
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28
questions
1
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0answers
21 views
How does decrease the size of “grey” module in WGCNA framework?
Relate to finding soft power, I ran "pickSoftThreshold" function and the result of that(sft) is as follow:
...
0
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0answers
17 views
How to analyze the correlation of two different tissue gene expression under three conditions?
I have three conditions A, B, and C. For each state, I have gene expression data of two different tissues(liver and pancreas). I am studying the possible network/correlation/ between tissues for each ...
1
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1answer
20 views
Does module size decrease as the number of samples increase in WGCNA?
We are working with a lot of samples, more than 50,000 people! We are using WGCNA to get modules and it seems like there are less number of module genes the more people we use. We are following the ...
0
votes
1answer
27 views
Running GSEA or comparable analysis with multiple variable interaction?
I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the interaction between two variables, one (INJ) with two conditions (L,S) and the ...
3
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0answers
67 views
How to calculate module-trait relationship when trait data is in binary format?
I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
1
vote
1answer
94 views
Which module to select for Pathway analysis based on Module trait correlation and pvalue?
I have a total of 35 tumor samples classified into 4 subtypes. Subtype A, B, C, and D. I have RNAseq data. I'm interested in identifying modules related to each subtype with co-expression network ...
0
votes
1answer
87 views
WGCNA co-expression network analysis with less than 20 samples
I have two cancer subtypes data. Subtype A is 14 samples and Subtype B is 23 samples. I'm interested in identifying the functions of some LncRNAs in the Subtype A group. For this I'm using all protein-...
1
vote
0answers
53 views
exportNetworkToCytoscape in WGCNA in R for a large network
I created a co-expression network for my data using WGCNA in R. I am trying to export my co-expression network into Cytoscape readable format using ...
1
vote
1answer
35 views
Weighted Network Analysis Book by Steve Horvath, taking the power of a matrix
In Horvath's Weighted network analysis, the author mentions that M^b, where b is a real number and M is a matrix, denotes the element-wise power. This seems odd to me. The way I was taught, M^b would ...
0
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1answer
47 views
Speeding up network creation in WGCNA
I am following the tutorials on the WGCNA website for creating a coexpression network. It is taking way too long. Is there a way to speed up execution? All I need is to create the co-expression graph. ...
1
vote
1answer
140 views
Importing a WGCNA co-expression network into a networkX graph in Python
Is there a way to generate a WGCNA co-expression graph in R, and then to import that graph into Python such that I can represent it using a networkX object?
2
votes
1answer
127 views
Identifying mutually **exclusive** gene sets
I am interested in identifying gene pairs (or better: sets of genes) whose expression is mutually exclusive.
Ideally, both genes (or gene sets) would be widely expressed but I am also interested in ...
0
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1answer
492 views
WGCNA: Problem with selecting soft threshold
I have 25 tumor samples with counts data. Initially, I filtered out low expressed genes and then converted counts to varianceStabilizingTransformation using ...
-1
votes
1answer
43 views
Module preservation and hub genes finding
I ran module preservation analysis between two condition and on the basis of preservation z summary i would to go for downstream analysis.So I m interested in looking for hub-genes of those modules ...
0
votes
1answer
42 views
Parallelizing WGCNA k-means clustering and merging smaller clusters
WGCNA carefully takes advantage of server parallelization in several functions, and I can switch this on with:
enableWGCNAThreads(nThreads=28)
That speeds up ...
0
votes
1answer
33 views
Tree cut height for Consensus data input not working
I have tried different combination of tree cut heights but im getting the exprSize as one sample as full the other one as empty .
...
-1
votes
1answer
178 views
WGCNA module preservation doubt
The WGCNA analysis page48 of that link.
In this analysis they are comparing the Preservation of modules between human and chimpanzee brain networks where i see the number of human modules and chimp ...
0
votes
1answer
73 views
WGCNA correcting p value for varying sample numbers in each of the trait columns
I am correcting a data frame of sample comparison using p value. However in some columns I have different sample numbers. Within the data frame I have 4 comparisons e.g B_R, R_C, B_C, C_C. They each ...
0
votes
1answer
20 views
WGCNA module preservation error code with plotting summary statistics
I am trying module preservation with WGCNA using my own data. I am plotting the summary statistics including Zsummary, medianRank, observed IGP and IGP permutation p-value for two comparison data sets....
1
vote
1answer
55 views
WGCNA module preservation
I am completing the online tutorials for module preservation of human brain modules in chimpanzee brains and vice versa (III). If anyone is aware of this tutorial or practiced before wondering if can ...
0
votes
1answer
118 views
WGCNA module preservation analysis
I have case control studies,4 different condition where I have 1 control and against which I'm have 3 comparisons to make.
I did WGCNA for individuals samples .Here I have the kept the number of ...
0
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1answer
115 views
0
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2answers
170 views
R WGCNA error code
I am using WGCNA to identify Consensus modules. I get a warning message when completing the following step:
Call the network topology analysis function for each set in turn
Warning:
...
1
vote
0answers
129 views
module differential connectivity (MDC) analysis
Paper in this paper I am citing the lines below .
) Intra-modular connectivity of resilient and susceptible network modules was compared to that of corresponding genes in control mice to identify ...
2
votes
1answer
317 views
Hierarchical clustering for outlier detection - single cell RNASeq & WGCNA
I wish to conduct WGCNA on a single cell RNASeq dataset and, when choosing the optimal beta parameter after running pickSoftThreshold am presented with a rather ...
1
vote
1answer
347 views
Error Code in WGCNA: Dealing with large data sets: block-wise network construction andmodule detection
I am comparing single block module detection with 2 block module detection in WGCNA.
Does anyone know what this relates to? I have rechecked and rechecked my codes for both the single and 2 module ...
1
vote
1answer
184 views
WGCNA error codes in Network Construction & moduel detection
I am using WGCNA and code has worked with no problems with some of my datasets however with most recent attempt when completing gene network & identification of modules. I get following error code....
2
votes
3answers
219 views
Question about Co-expression analysis and finding targets for lncRNAs
I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs)
I wanted to do co-expression analysis between ...
