User: christopher.clarskon15

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Posts by christopher.clarskon15

<prev • 28 results • page 1 of 3 • next >
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Answer: A: Error in for 'x' has a zero dimension WGCNA
... Thank you Keith the error that results when I try to print the dim of the file that's being uploaded is:  Error in UseMethod: no applicable method for 'xtable' applied to an object of class "c('integer', 'numeric')" ...
written 16 months ago by christopher.clarskon1520
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Error in for 'x' has a zero dimension WGCNA
... I am developing a shiny application to implement a WGCNA pipeline. In my 'server' script I am using the following code: adjacentmat<-reactive({adjacency(dataInput1(),power=input$num)})   Having uploaded the data expression file to the website (of dim, 1:8000,1:200), I get the following error: ...
wgcna R written 16 months ago by christopher.clarskon1520
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Comment: C: Re : zero dimension error while soft thresholding in wgcna
... I have this same problem only for the command 'cor': Error in for 'x' has a zero dimension ...
written 16 months ago by christopher.clarskon1520
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Answer: A: interactive networks from WGCNA clusters
... The following code allowed me to colour the nodes according to their blockGene...  net = blockwiseModules(E.rna_small, maxBlockSize = 2000,                          power = 6, TOMType = "unsigned", minModuleSize = 2,                          reassignThreshold = 0, mergeCutHeight = 0.25,             ...
written 16 months ago by christopher.clarskon1520
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interactive networks from WGCNA clusters
...   I am trying to get an interactive network to deploy from a pipeline of WGCNA steps. I would like to be able to upload a file that can be read into a data frame and processed to make a network. Below is the code that I have used to identify modules in the gene-network: p1<-adjacency(E.rna_smal ...
rcytoscape wgcna written 16 months ago by christopher.clarskon1520 • updated 16 months ago by branislav misovic120
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Comment: C: WGCNA network visualisation in RCyjs
... Further Development: I have used the following code to make an RCyjs graph: rcy <- RCyjs(portRange=9047:9057, quiet=TRUE, graph=igraph.to.graphNEL(graph_from_adjacency_matrix(p1, weighted=T))) I am yet to check if the graph is congruent with the one that I originally plotted in Rstudio with the ...
written 17 months ago by christopher.clarskon1520
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Comment: C: WGCNA network visualisation in RCyjs
... Hi Paul, Thanks for the reply all i'm doing is running a pearsson correlation on a 20x20 matrix as follows: p1<-cor(t(E.rna[1:20,1:20]),use="p") Then with the 'network' package and 'graph' package as per your recommendation i tried the following: graphNEL(as.network.matrix(p1)) But i get th ...
written 17 months ago by christopher.clarskon1520
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WGCNA network visualisation in RCyjs
... I have used the Pearson correlation method to infer a network of interacting genes from microarray data. And ultimately, I would like to study this network with 'WGCNA'. However as useful as some of the commands in WGCNA seem, I can't find anywhere in the tutorials a command that actually allows me ...
rcytoscape wgcna network analysis written 17 months ago by christopher.clarskon1520 • updated 17 months ago by Paul Shannon360
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Answer: A: limma overfitting model due to intercept and yet exclusion of intercept= uninter
... Hi James, the design matrix was created as follows: design <- cbind(1, as.numeric(as.factor(clinical1$Sex)), clinical1$Age..mths. ) colnames(design)=c("Intercept", "Sex", "Age") Other<-ifelse(clinical1$Diagnostic.category=="Other diagnoses", 1,0) TB<-ifelse(clinical1$Diagnostic.category== ...
written 18 months ago by christopher.clarskon1520
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limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
... I have microarray data for which the columns represent the disease condition status of each individual. I plan to fit a linear model and then make a contrast amongst the different columns using limma. My question is: how do I make the most informative comparison when contrasting all of the columns ...

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