Questions tagged [wgcna]
The wgcna tag has no usage guidance.
31
questions
0
votes
0
answers
19
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 ...
1
vote
0
answers
32
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 ...
2
votes
1
answer
39
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
votes
1
answer
44
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 ...
0
votes
1
answer
139
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:
...
1
vote
0
answers
149
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
241
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
96
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 ...
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 ...
0
votes
1
answer
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 ...
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-...
1
vote
1
answer
41
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
110
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
246
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
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 ...
0
votes
1
answer
1k
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
59
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
84
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
47
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
383
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
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 ...
0
votes
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....
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 ...
0
votes
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 ...
0
votes
1
answer
232
views
0
votes
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:
...
1
vote
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, ...
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 ...
1
vote
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 ...
1
vote
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....
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 ...