Questions tagged [wgcna]

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35 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 ...
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0answers
13 views

WGCNA error in labeledHeatmap

I have a large RNA-seq dataset with multiple samples. I am doing network analysis using WGCNA. I got an error while making phenotype module relationship matrix. The code I am using: ...
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1answer
77 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 ...
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1answer
36 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-...
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0answers
29 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 ...
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1answer
31 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
32 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
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1answer
57 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
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1answer
120 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
191 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 ...
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1answer
41 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 ...
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1answer
22 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 ...
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1answer
31 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
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1answer
87 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 ...
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1answer
48 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 ...
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1answer
15 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....
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0answers
11 views

WGCNA R correction for different sample sizes in module trait comparison

I am doing WGCNA analysis and relating modules to external traits. Within my sample I have 51 samples in one trait or interest, 49 in another trait of interest and 48 in the 3rd trait of interest. I ...
1
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1answer
42 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
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1answer
76 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
72 views

Tree cut issue in WGCNA

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2answers
87 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: ...
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0answers
83 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 ...
1
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1answer
253 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
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1answer
190 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
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1answer
167 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
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3answers
204 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 ...