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bk11
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@bk11-19547
Last seen 3.7 years ago
Hi
I am running through this tutorial https://f1000research.com/articles/5-2122/v1. But I got this error. I m new to single cell experiment. Why newSCESet(countData=all.counts)
function not working? I will appreciate your help. Thanks.
I have used these codes:
library(R.utils)
gunzip("GSE61533_HTSEQ_count_results.xls.gz", remove=FALSE, overwrite=TRUE)
library(gdata)
all.counts <- read.xls(’GSE61533_HTSEQ_count_results.xls’, sheet=1, header=TRUE, row.names=1)
library(scater)
sce <- newSCESet(countData=all.counts)
It gave me error:
Error in newSCESet(countData = all.counts) :
could not find function "newSCESet"
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
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] simpleSingleCell_1.4.1 TENxBrainData_1.2.0 HDF5Array_1.10.1
[4] rhdf5_2.26.2 BiocNeighbors_1.0.0 BiocFileCache_1.6.0
[7] dbplyr_1.3.0 DropletUtils_1.2.2 scRNAseq_1.8.0
[10] TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0 GenomicFeatures_1.34.1 edgeR_3.24.3
[13] cluster_2.0.7-1 dynamicTreeCut_1.63-1 pheatmap_1.0.12
[16] limma_3.38.3 scran_1.10.2 org.Mm.eg.db_3.7.0
[19] AnnotationDbi_1.44.0 readxl_1.2.0 destiny_2.12.0
[22] mvoutlier_2.0.9 sgeostat_1.0-27 Rtsne_0.15
[25] knitr_1.21 BiocStyle_2.10.0 scater_1.10.1
[28] ggplot2_3.1.0 SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0
[31] DelayedArray_0.8.0 BiocParallel_1.16.5 matrixStats_0.54.0
[34] Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.1
[37] IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
[40] gdata_2.18.0 R.utils_2.7.0 R.oo_1.22.0
[43] R.methodsS3_1.7.1 updateR_0.1 magrittr_1.5
[46] stringr_1.3.1 rvest_0.3.2 xml2_1.2.0
[49] dplyr_0.7.8 usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.1 rtracklayer_1.42.1 ggthemes_4.0.1
[4] prabclus_2.2-7 GGally_1.4.0 bit64_0.9-7
[7] data.table_1.12.0 RCurl_1.95-4.11 callr_3.1.1
[10] RSQLite_2.1.1 proxy_0.4-22 bit_1.1-14
[13] httpuv_1.4.5.1 assertthat_0.2.0 viridis_0.5.1
[16] xfun_0.4 hms_0.4.2 promises_1.0.1
[19] evaluate_0.12 DEoptimR_1.0-8 progress_1.2.0
[22] igraph_1.2.2 DBI_1.0.0 reshape_0.8.8
[25] purrr_0.2.5 selectr_0.4-1 backports_1.1.3
[28] trimcluster_0.1-2.1 sROC_0.1-2 biomaRt_2.38.0
[31] remotes_2.0.2 TTR_0.23-4 abind_1.4-5
[34] RcppEigen_0.3.3.5.0 withr_2.1.2 robustbase_0.93-3
[37] vcd_1.4-4 GenomicAlignments_1.18.1 xts_0.11-2
[40] prettyunits_1.0.2 mclust_5.4.2 ExperimentHub_1.8.0
[43] lazyeval_0.2.1 laeken_0.5.0 crayon_1.3.4
[46] pkgconfig_2.0.2 zCompositions_1.1.2 vipor_0.4.5
[49] pkgload_1.0.2 nnet_7.3-12 bindr_0.1.1
[52] rlang_0.3.1 diptest_0.75-7 pls_2.7-0
[55] AnnotationHub_2.14.2 cellranger_1.1.0 rprojroot_1.3-2
[58] lmtest_0.9-36 Matrix_1.2-15 carData_3.0-2
[61] Rhdf5lib_1.4.2 boot_1.3-20 zoo_1.8-4
[64] beeswarm_0.2.3 processx_3.2.1 viridisLite_0.3.0
[67] bitops_1.0-6 Biostrings_2.50.2 blob_1.1.1
[70] DelayedMatrixStats_1.4.0 scales_1.0.0 memoise_1.1.0
[73] plyr_1.8.4 zlibbioc_1.28.0 compiler_3.5.1
[76] RColorBrewer_1.1-2 rrcov_1.4-7 Rsamtools_1.34.0
[79] cli_1.0.1 XVector_0.22.0 ps_1.3.0
[82] MASS_7.3-51.1 tidyselect_0.2.5 stringi_1.2.4
[85] forcats_0.3.0 yaml_2.2.0 locfit_1.5-9.1
[88] grid_3.5.1 tools_3.5.1 rio_0.5.16
[91] rstudioapi_0.9.0 foreign_0.8-71 gridExtra_2.3
[94] smoother_1.1 scatterplot3d_0.3-41 digest_0.6.18
[97] BiocManager_1.30.4 shiny_1.2.0 fpc_2.1-11.1
[100] bindrcpp_0.2.2 Rcpp_1.0.0 car_3.0-2
[103] later_0.7.5 httr_1.4.0 kernlab_0.9-27
[106] colorspace_1.4-0 XML_3.98-1.16 fs_1.2.6
[109] truncnorm_1.0-8 splines_3.5.1 statmod_1.4.30
[112] sp_1.3-1 flexmix_2.3-14 sessioninfo_1.1.1
[115] xtable_1.8-3 modeltools_0.2-22 R6_2.3.0
[118] NADA_1.6-1 mime_0.6 pillar_1.3.1
[121] htmltools_0.3.6 glue_1.3.0 VIM_4.7.0
[124] cvTools_0.3.2 class_7.3-15 interactiveDisplayBase_1.20.0
[127] pkgbuild_1.0.2 pcaPP_1.9-73 mvtnorm_1.0-8
[130] lattice_0.20-38 tibble_2.0.1 curl_3.3
[133] ggbeeswarm_0.6.0 gtools_3.8.1 zip_1.0.0
[136] openxlsx_4.1.0 survival_2.43-3 rmarkdown_1.11
[139] desc_1.2.0 munsell_0.5.0 e1071_1.7-0.1
[142] GenomeInfoDbData_1.2.0 haven_2.0.0 reshape2_1.4.3
[145] gtable_0.2.0 robCompositions_2.0.9
I have tried this workflow and still getting the same error
You must be following along with an older version of the workflow than the current one (which Aaron linked to). As far as I know, the
newSCEsetstuff has been completely replaced by usingSingleCellExperimentobjects.You should make sure that you are reading the "release" version of these workflows, as well as the current (release) version of the Bioconductor ecosystem (v3.8) -- which you can check using the following R code
packageVersion("BiocVersion")[,1:2].(edit)
I see from you sessionInfo that you are using the release versions of bioc software -- so I'm guessing you are just looking at outdated code somewhere ... again, you should be using the relase version of the simpleSingleCell worfklow (if that's the code you are following along with).