Question: Problem in WGCNA soft thresholding
0
gravatar for tryjpark
12 months ago by
tryjpark0
tryjpark0 wrote:

Hello.

I'm studying on R and WGCNA. R version 3.6.1.

Starting with tutorial, I didn't have any problems in contructing network. I was able to plot the network figure for Liverfemale3600.csv file.

However, when I tried to do same for my data, R returned error at soft-thresholding step like this;

P.S I have just copy-and-pasted my sample data to tutorial csv file.

library(WGCNA);
>dynamicTreeCut
>fastcluster
>'fastcluster'
>The following object is masked from 'package:stats':
>hclust
>: 'WGCNA'
>The following object is masked from 'package:stats':
>cor
options(stringsAsFactors = FALSE);
enableWGCNAThreads()
>Allowing parallel execution with up to 3 working processes.
lnames = load(file = "mydat-01-dataInput.RData");
lnames
>[1] "datExpr"
dim(datExpr);
>[1]    0 5000
powers = c(c(1:10), seq(from = 12, to=20, by=2))
sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)
>pickSoftThreshold: will use block size 5000.
>pickSoftThreshold: calculating connectivity for given powers...
>   ..working on genes 1 through 5000 of 5000
>Error in { : task 1 failed - "'x' has a zero dimension."

As shown, I am stuck and cannot solve the error... I'm sure that my expression data has all numeric values. I assumed that this problem is associated with below situation..

dim(datExpr);

>[1]    0 5000

Could anyone advice me to solve this problem?

Please help TT

R wgcna • 419 views
ADD COMMENTlink modified 12 months ago by WouterDeCoster44k • written 12 months ago by tryjpark0
1

The error message is indeed quite explicit and you've found the cause: datExpr doesn't have any row. Check that your data is what it should be.

ADD REPLYlink written 12 months ago by Jean-Karim Heriche23k
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