Questions tagged [wgcna]

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NEO analysis tutorial and data

I was reading Jason Aten's paper Using genetic markers to orient the edges in quantitative trait networks: The NEO software, which states The NEO software can be used to orient the edges of gene co-...
1 vote
1 answer
17 views

WGCNA soft threshold selection

Here I am conducting WGCNA analysis. When calculating the soft threshold, it is basically below 0.8. I choose Power=6, which only has 0 and 7. Is it feasible?
1 vote
1 answer
43 views

Extracting P-Values for Co-Expressed Genes Within WGCNA Modules

I'm facing a challenge regarding the extraction of co-expressing genes from each module. After identifying modules, I've been using exportNetworkToCytoscape to visualize genes that co-express together....
2 votes
1 answer
74 views

WGCNA: Extract genes within the different modules to create a dataframe with two columns

My inquiry pertains to WGCNA. After identifying the modules, I would like to extract genes within the different modules to create a dataframe with two columns: ...
0 votes
1 answer
68 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....
3 votes
1 answer
1k views

Where to access the WGCNA tutorial documents: Horvath lab site down

I am currently using the WGCNA package for some analysis and it seems the Horvath lab site is down. Does anyone know of anywhere else I can access the tutorial documents?
2 votes
1 answer
53 views

How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?

I am working on using WGCNA for a bulk RNA-seq experiment. I have three experimental conditions (control, treatment 1, and treatment 2) and have a total sample size of 18 (6 per group). Using the ...
2 votes
1 answer
434 views

Tutorial for the WGCNA: changes in heatmap colours

I am trying to reproduce the results of the R tutorial of the WGCNA package. In section I number 5, when generating the heatmap it is quite similar to the one provided by the pdf but the colours of ...
-1 votes
1 answer
368 views

WGCNA error: Length of colors vector not compatible with number of objects in 'order'

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1 vote
1 answer
335 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 ...
1 vote
1 answer
301 views

WGCNA hub genes error

I am trying to find hub genes for modules made using WGCNA: hub = chooseTopHubInEachModule(datExpr, moduleColors) But I am getting error: ...
2 votes
1 answer
105 views

Coexpression network analysis

I have a question related with the most popular frameworks for network construction: WGCNA for weighted networks and igraph package for unweighted networks. What are the advantages or disadvantages of ...
0 votes
1 answer
141 views

How to find closely related genes for a specific gene from WGCNA modules?

I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules. Among all ...
0 votes
2 answers
240 views

Is it possible to integrate multiple gene expression datasets and use it for WGCNA?

I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene. Among 8 RNA-seq datasets, 6 have less than 20 samples. Rather than working on each dataset ...
3 votes
1 answer
181 views

How to improve this WGCNA analysis

This is my first time working on using WGCNA on a microarray dataset. One of the major problems I am facing is merging close modules which is not really working well. I have quantile normalised the ...
2 votes
2 answers
64 views

WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low

I'm doing a WCGNA analysis (signed network) on microbiome 16S data. I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and ...
1 vote
1 answer
42 views

How can to validate the presence of a certain type of cells in a single cell dataset?

I have a single cell dataset which I consider to be a reference , let say, for an human organ, I have identified some new clusters that correspond to cell types. I also have WGCNA modules that ...
1 vote
0 answers
195 views

How to assess quality of WGCNA module identification in blockwisemodules()

I'm exploring WGCNA for bulkRNA sequencing analysis with human subjects. I have healthy, myocarditis, and heart failure patients (which can be further broken into ischemic or nonischemic) I have been ...
2 votes
1 answer
63 views

Find enriched processes in modules obtained by WGCNA

I am doing a gene enrichment of different clusters obtained by WGCNA, but there are some of them in which I don't get enriched processes, is there any way to find processes to these modules, for ...
1 vote
1 answer
287 views

module differential connectivity (MDC) analysis

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 gain, loss, ...
4 votes
1 answer
437 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 votes
1 answer
64 views

no expression for hub genes identified in wgcna

I tried to identify intramodular hub genes in WGCNA analysis. I used: hub = chooseTopHubInEachModule(datExpr, moduleColors) But ...
1 vote
0 answers
420 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 votes
1 answer
746 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
1 answer
150 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 ...
1 vote
1 answer
422 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
1 answer
45 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 votes
1 answer
209 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
1 answer
294 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
1 answer
189 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 votes
1 answer
2k 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
1 answer
80 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
1 answer
133 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
1 answer
61 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
1 answer
576 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
1 answer
261 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 ...
1 vote
1 answer
117 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
1 answer
415 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 votes
1 answer
335 views

Tree cut issue in WGCNA

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0 votes
2 answers
1k 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
1 answer
568 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
1 answer
1k 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
1 answer
253 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
3 answers
248 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 ...