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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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number of cells does not match number of labels #7

Closed djchin25 closed 6 years ago

djchin25 commented 6 years ago

Getting an error about 'number of cells' not matching the number of cells despite length(labels) = number of cells

scimpute(count_path, infile, outfile, out_dir, labeled = TRUE, drop_thre, Kcluster, ncores) [1] "reading in raw count matrix ..." [1] "number of genes in raw count matrix 33694" [1] "number of cells in raw count matrix 8055" Error in scimpute(count_path, infile, outfile, out_dir, labeled = TRUE, : number of cells does not match number of labels ! length(labels) [1] 8055 table(labels) labels c1 c2 c3 1174 4909 1972

######################## sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] scImpute_0.0.4 doParallel_1.0.11 iterators_1.0.9 foreach_1.4.4 penalized_0.9-50 [6] survival_2.41-3 kernlab_0.9-25

loaded via a namespace (and not attached): [1] compiler_3.4.1 Matrix_1.2-11 tools_3.4.1 Rcpp_0.12.14 codetools_0.2-15 [6] splines_3.4.1 grid_3.4.1 lattice_0.20-35

djchin25 commented 6 years ago

found my error: needed labels=labels