error when running run.scWGCNA
Opened this issue · 2 comments
Hello, I am running scWGCNA on my own dataset, everything seems fine to generate a pseudocell dataset, and it stucks withthe next step.
here is my dataset:
> c5
An object of class Seurat
24950 features across 2449 samples within 3 assays
Active assay: integrated (3000 features, 3000 variable features)
2 other assays present: RNA, SCT
3 dimensional reductions calculated: pca, tsne, umap
This dataset was integrated with CCA, and only the "integrated assay" can be used to produce the pseudo cell dataset.
here is my pseudo cell dataset:
> c5.pcells
An object of class Seurat
24950 features across 489 samples within 3 assays
Active assay: integrated (3000 features, 0 variable features)
2 other assays present: RNA, SCT
and here is the running message:
> c5.scWGCNA = run.scWGCNA(p.cells = c5.pcells, # Pseudocells (recommended), or Seurat single cells
+ s.cells = c5, # single cells in Seurat format
+ is.pseudocell = T, # We are using single cells twice this time
+ features = rownames(c5)) # Recommended: variable genes
[1] "The following variable genes were not found expressed in the pseudocell object: "
[1] "We have 3000 genes in the variable genes object"
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 1 0.00603 -1.10 0.875 1.64e+03 1.65e+03 1900.00
2 2 0.11500 -2.51 0.890 9.10e+02 9.16e+02 1230.00
3 3 0.27600 -2.81 0.924 5.11e+02 5.15e+02 816.00
4 4 0.43200 -2.84 0.947 2.91e+02 2.92e+02 553.00
5 5 0.54100 -2.81 0.938 1.68e+02 1.67e+02 381.00
6 6 0.63200 -2.81 0.944 9.79e+01 9.67e+01 268.00
7 7 0.69700 -2.80 0.967 5.79e+01 5.65e+01 191.00
8 8 0.73900 -2.65 0.960 3.47e+01 3.33e+01 139.00
9 9 0.78900 -2.66 0.934 2.10e+01 1.98e+01 103.00
10 10 0.84600 -2.76 0.914 1.29e+01 1.18e+01 76.90
11 12 0.95300 -2.84 0.964 5.03e+00 4.31e+00 45.30
12 14 0.96200 -2.67 0.953 2.06e+00 1.61e+00 28.30
13 16 0.96700 -2.42 0.958 8.85e-01 6.20e-01 18.80
14 18 0.94800 -2.19 0.935 4.01e-01 2.43e-01 13.20
15 20 0.43900 -2.74 0.340 1.92e-01 9.74e-02 9.67
16 22 0.43700 -2.47 0.341 9.78e-02 3.96e-02 7.35
17 24 0.32800 -2.50 0.141 5.31e-02 1.65e-02 5.75
18 26 0.43500 -2.09 0.351 3.08e-02 6.93e-03 4.61
19 28 0.39400 -2.34 0.328 1.91e-02 2.98e-03 3.78
20 30 0.39600 -2.21 0.334 1.26e-02 1.30e-03 3.14
[1] "Or power is 12"
TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[1] "my.height: 0.9993 .... my.Clsize: 15"
202 genes not assigned to any module.
2606 genes excluded due to significance.TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[1] "my.height: 0.9995 .... my.Clsize: 15"
25 genes not assigned to any module.
144 genes excluded due to significance.TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[1] "my.height: 0.9989 .... my.Clsize: 21"
2 genes not assigned to any module.
13 genes excluded due to significance.TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Error in seq.default(cutheight - 5e-04, cutheight + 5e-04, 1e-04) :
'from' must be of length 1
I googled and cannot find a solution to this error. Any help will be appreciated.
Best,
Xue
Hello, sorry that I am only coming back to this. I've been rather busy.
I think I see what the problem is, it looks like your modules might be all to similar. I'll try to reproduce the error and fix it.
Is there a reason why the tutorial is able to run on SCT assays and here we (I also face same problem which limits the assay type I can run on) have to run on integrated datasets?