Questions tagged [wgcna]

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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 ...
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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 ...
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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 ...
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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 ...
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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: ...
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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: ...
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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 ...
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1 answer
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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 ...
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4 votes
1 answer
153 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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168 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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1 vote
1 answer
235 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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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 ...
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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. ...
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1 answer
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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?
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2 votes
1 answer
170 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 ...
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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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1 answer
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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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1 answer
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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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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 . ...
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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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1 answer
147 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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1 answer
31 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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1 vote
1 answer
97 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 ...
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1 answer
240 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 ...
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1 answer
232 views

Tree cut issue in WGCNA

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2 answers
517 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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1 answer
201 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, ...
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1 vote
1 answer
444 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 ...
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1 answer
733 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 ...
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1 answer
222 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....
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2 votes
3 answers
239 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 ...
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