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SCA-IRCM / SingleCellSignalR_v1

R package
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Error while clustering #7

Closed singcell closed 4 years ago

singcell commented 4 years ago

I am using matrix file generated by 'Read10x' function to input in data_prepare. I get following data_prepare output:

data <- data_prepare(file=file, most.variables = 2000,write = TRUE) log-Normalization 15200 genes 14267 cells Zero rate = 91.2% Warning message: In fread(file, data.table = FALSE) : Detected 14267 column names but the data has 14268 columns (i.e. invalid file). Added 1 extra default column name for the first column which is guessed to be row names or an index. Use setnames() afterwards if this guess is not correct, or fix the file write command that created the file to create a valid file.

looks like previous step log-normalized and If I overlook this warning message and go over to clustering command, I get following Error:

clust <- clustering(data = data, n = 10, method = "simlr") Estimating the number of clusters Error in x^2 : non-numeric argument to binary operator

Would it be possible for you to diagnose the problem?

Thank you.

SCA-IRCM commented 4 years ago

Hi, I advise you not to combine the pre-processing steps from different tools (Seurat and SingleCellSignalR). If you want to use Seurat for pre-processing, do the log normalization steps before extracting the counts matrix (see https://github.com/SCA-IRCM/Demo/blob/master/example_seurat.R) to feed the clustering function of SingleCellSignalR. Thank you for using SingleCellSignalR.

SCA