Hello everyone
I am doing network analyses by using WGCNA, I got error message when I am setting the soft threshold. Here is what I got.
I am following these commands:
> library(WGCNA)
disableWGCNAThreads()
> library(cluster)
> options(stringsAsFactors = FALSE)
> femData = read.csv("gene.csv")
> names(femData)
[1] "gene_id" "gene" "locus" "log2.fold_change."
[5] "test_stat" "p_value" "q_value" "AF"
[9] "AF.1" "AF.2" "AD" "AD.1"
[13] "AD.2"
> dim(femData)
[1] 6765 13
> datExprFemale=as.data.frame(t(femData[, -c(1:7)]))
> names(datExprFemale)=femData$gene
> rownames(datExprFemale)=names(femData)[-c(1:7)]
> powers=c(1:10)
> sft=pickSoftThreshold(datExprFemale,powerVector=powers)
Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds
In addition: Warning message:
executing %dopar% sequentially: no parallel backend registered
I tried to find similar questions in archive, but I could not.
Please I need help with this issue if anyone able to help.
Best
Shaima
1 answer
The error means you're trying to access an element outside the array; this usually means one your indices is greater than the last available index of the array.
As for the warning, check the doParallel docs: "Remember: unless registerDoMC is called, foreach will not run in parallel. Simply loading the doParallel package is not enough."
It's all in the docs I linked to above. Basically, all you need is
library(doParallel);
registerDoParallel(cores= x);
where x is the number of cores/workers you want to use. Note that this is only worthwhile for relatively lengthy computations as creating parallel workers is expensive and can take longer than running a fast bit of code.
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@saj98 Can you please give an example of your data so we can reproduce your problem and try to solve it?
I am following these commands:
For the warning message:
Have you tried the allowWGCNAThreads() function?
Yes I did, but I got the same error.
Are you trying to perform WGCNA analysis with 6 samples?
Yes I am doing six samples.