尝试制作singleR seurat对象时出错

时间:2019-02-06 21:17:00

标签: r error-messaging

我一直在尝试解决此问题,但整天都空着。尝试制作此对象

singleR = CreateSinglerSeuratObject(counts = counts, 
                                    annot = metadata, 
                                    project.name = 'project', 
                                    min.genes = 1, 
                                    min.cells = 2, 
                                    npca = 5, 
                                    regress.out ='nUMI', 
                                    species = 'Mouse', 
                                    citation = '', 
                                    reduce.file.size = T, 
                                    variable.genes = 'de',
                                    normalize.gene.length = T, 
                                    numCores = 5)

我收到此错误代码:

  

irlba中的错误(A = t(x = data.use),nv = pcs.compute,...):     max(nu,nv)必须严格小于min(nrow(A),ncol(A))

我的计数是[6 x 13732]的矩阵。

session info():
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Seurat_2.3.4                Matrix_1.2-15               cowplot_0.9.4              
 [4] ggplot2_3.1.0               SingleR_0.2.0               DESeq2_1.21.23             
 [7] SummarizedExperiment_1.11.6 DelayedArray_0.7.48         BiocParallel_1.15.15       
[10] matrixStats_0.54.0          Biobase_2.41.2              GenomicRanges_1.33.14      
[13] GenomeInfoDb_1.17.3         IRanges_2.15.18             S4Vectors_0.19.22          
[16] BiocGenerics_0.27.1        

loaded via a namespace (and not attached):
  [1] snow_0.4-3             backports_1.1.3        Hmisc_4.2-0            plyr_1.8.4            
  [5] igraph_1.2.2           lazyeval_0.2.1         GSEABase_1.43.1        splines_3.5.1         
  [9] listenv_0.7.0          digest_0.6.18          foreach_1.4.4          htmltools_0.3.6       
 [13] lars_1.2               gdata_2.18.0           magrittr_1.5           checkmate_1.9.1       
 [17] memoise_1.1.0          cluster_2.0.7-1        mixtools_1.1.0         ROCR_1.0-7            
 [21] globals_0.12.4         annotate_1.59.1        R.utils_2.7.0          colorspace_1.4-0      
 [25] blob_1.1.1             xfun_0.4               dplyr_0.7.8            crayon_1.3.4          
 [29] RCurl_1.95-4.11        jsonlite_1.6           graph_1.59.2           genefilter_1.63.2     
 [33] bindr_0.1.1            survival_2.43-3        zoo_1.8-4              iterators_1.0.10      
 [37] ape_5.2                glue_1.3.0             gtable_0.2.0           zlibbioc_1.27.0       
 [41] XVector_0.21.4         kernlab_0.9-27         prabclus_2.2-7         DEoptimR_1.0-8        
 [45] scales_1.0.0           pheatmap_1.0.12        mvtnorm_1.0-8          DBI_1.0.0             
 [49] bibtex_0.4.2           Rcpp_1.0.0             metap_1.0              dtw_1.20-1            
 [53] xtable_1.8-3           htmlTable_1.13.1       reticulate_1.10        foreign_0.8-71        
 [57] bit_1.1-14             proxy_0.4-22           mclust_5.4.2           SDMTools_1.1-221      
 [61] Formula_1.2-3          GSVA_1.29.3            tsne_0.1-3             htmlwidgets_1.3       
 [65] httr_1.4.0             gplots_3.0.1.1         RColorBrewer_1.1-2     fpc_2.1-11.1          
 [69] acepack_1.4.1          modeltools_0.2-22      ica_1.0-2              pkgconfig_2.0.2       
 [73] XML_3.98-1.16          R.methodsS3_1.7.1      flexmix_2.3-14         nnet_7.3-12           
 [77] locfit_1.5-9.1         later_0.7.5            tidyselect_0.2.5       rlang_0.3.1           
 [81] reshape2_1.4.3         AnnotationDbi_1.43.1   pbmcapply_1.3.1        munsell_0.5.0         
 [85] tools_3.5.1            RSQLite_2.1.1          ggridges_0.5.1         stringr_1.3.1         
 [89] yaml_2.2.0             npsurv_0.4-0           outliers_0.14          knitr_1.21            
 [93] bit64_0.9-7            fitdistrplus_1.0-14    robustbase_0.93-3      caTools_1.17.1.1      
 [97] purrr_0.2.5            RANN_2.6.1             bindrcpp_0.2.2         future_1.11.1.1       
[101] pbapply_1.3-4          nlme_3.1-137           mime_0.6               R.oo_1.22.0           
[105] shinythemes_1.1.2      hdf5r_1.0.1            compiler_3.5.1         rstudioapi_0.9.0      
[109] png_0.1-7              lsei_1.2-0             tibble_2.0.1           geneplotter_1.59.0    
[113] stringi_1.2.4          lattice_0.20-38        trimcluster_0.1-2.1    pillar_1.3.1          
[117] Rdpack_0.10-1          lmtest_0.9-36          data.table_1.12.0      bitops_1.0-6          
[121] irlba_2.3.2            gbRd_0.4-11            httpuv_1.4.5.1         R6_2.3.0              
[125] latticeExtra_0.6-28    promises_1.0.1         KernSmooth_2.23-15     gridExtra_2.3         
[129] codetools_0.2-16       MASS_7.3-51.1          gtools_3.8.1           assertthat_0.2.0      
[133] withr_2.1.2            GenomeInfoDbData_1.2.0 diptest_0.75-7         doSNOW_1.0.16         
[137] grid_3.5.1             rpart_4.1-13           tidyr_0.8.2            class_7.3-15          
[141] segmented_0.5-3.0      Rtsne_0.15             shiny_1.2.0            base64enc_0.1-3    

谢谢您的帮助!

0 个答案:

没有答案