Hi, I would like to use SAFE clustering on my single-cell dataset, but it seems the scripts are bugged. I tried to run the example provided on SAFE's website, but I'm getting this error.
Error in individual_clustering(inputTags = expr.mat, SEED = 123) :
(list) object cannot be coerced to type 'double' In addition: Warning message: 'newSCESet' is deprecated. Use 'SingleCellExperiment' instead. See help("Deprecated")
Here is the code I ran in order to obtain this error:
expr.mat <- read.csv("/home/snin/workspace/SAFE_clustering/expression_matrix.csv", header = T)
rownames(expr.mat) <- expr.mat[,1]
expr.mat <- expr.mat[,-1]
cluster.result <- individual_clustering(inputTags=expr.mat, SEED=123)
Can you maybe advise me to resolve this issue?
Have a nice day.
Chynoki
2 answers
Try
cluster.result <- individual_clustering(data.matrix(expr.mat), SEED=123)
If that does not work, then check your object to ensure that there are no characters in it. It has to be numeric. In some rare situations, a trailing space may appear after a number, in which case R will become confused. You can detect these by just converting the entire thing to text with:
as.character(expr.mat)
Hi, thanks for your answer.
I also contacted the dev of the tools and they told me the same. I used SAFEv1.0 instead of SAFEv2.0. Use SAFEv2.0 resolve my problem. It was the SCE package that were updated to v1.6 and SAFEv1.0 use SCEv1.3.
Now I have an other problem when running the tutorial.
This line:
ARI.SC3 = adjustedRandIndex(cluster[1,], celltype.info$cluster)
Give me the following error:
Error in as.vector(x) : object 'cluster' not found
I understand the error, but in the tutorial they do not instantiate a 'cluster' object.
I'm also waiting for an answer from the dev.
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