Questions tagged [wgcna]
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12
questions
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1answer
5 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
10 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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7 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
21 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
27 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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1answer
27 views
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2answers
28 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
28 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
108 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
67 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
121 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
163 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 ...
