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lmweber / FlowSOM-Rtsne-example

Worked example showing how to cluster and visualize flow/mass cytometry data using FlowSOM and Rtsne
MIT License
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error in out <- FlowSOM:BuildSOM() #1

Closed snowsummer closed 4 years ago

snowsummer commented 4 years ago

When run > out <- FlowSOM::BuildSOM(out, colsToUse = marker_cols) Building SOM Mapping data to SOM Error in if (length(y) > 0 && mean(y) != 0) { : missing value where TRUE/FALSE needed

lmweber commented 4 years ago

Hi, I would suggest having a look at the latest vignette from the FlowSOM package: http://bioconductor.org/packages/FlowSOM. There are probably some examples there that can show you how to run the latest version of FlowSOM.

malcook commented 4 years ago

@lmweber - I too am getting this error when running your very own code, run_FlowSOM.R, downloaded today from https://github.com/lmweber/cytometry-clustering-comparison.

So far as I can see nothing has changed in the interface to the FlowSOM package and you were and are calling it correctly.

I am seeking reproduce all the run_methods provided workflow from "Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data"

Can you possibly advise?

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /n/apps/CentOS7/install/r-3.6.1/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-3.6.1/lib64/R/lib/libRlapack.so

locale:
[1] C

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

other attached packages:
[1] FlowSOM_1.18.0  igraph_1.2.4.1  flowCore_1.52.0 devtools_2.2.1  usethis_1.5.1  

loaded via a namespace (and not attached):
 [1] tsne_0.1-3                  ncdfFlow_2.32.0             matrixStats_0.55.0          fs_1.3.1                    openCyto_1.24.0             RColorBrewer_1.1-2          rprojroot_1.3-2             Rgraphviz_2.30.0            tools_3.6.1                 backports_1.1.5             R6_2.4.0                    KernSmooth_2.23-16          BiocGenerics_0.32.0         colorspace_1.4-1            flowWorkspace_3.34.1        withr_2.1.2                 tidyselect_0.2.5            gridExtra_2.3               prettyunits_1.0.2           mnormt_1.5-5                processx_3.4.1             
[22] compiler_3.6.1              graph_1.64.0                cli_1.1.0                   Biobase_2.46.0              flowClust_3.24.0            ggcyto_1.14.1               desc_1.2.0                  flowStats_3.44.0            scales_1.0.0                DEoptimR_1.0-8              hexbin_1.27.3               mvtnorm_1.0-11              robustbase_0.93-5           callr_3.3.2                 RBGL_1.62.1                 stringr_1.4.0               digest_0.6.22               R.utils_2.9.0               rrcov_1.4-7                 base64enc_0.1-3             pkgconfig_2.0.3            
[43] sessioninfo_1.1.1           rlang_0.4.1                 jsonlite_1.6                gtools_3.8.1                mclust_5.4.5                dplyr_0.8.3                 R.oo_1.23.0                 magrittr_1.5                Matrix_1.2-17               Rcpp_1.0.2                  munsell_0.5.0               R.methodsS3_1.7.1           yaml_2.2.0                  stringi_1.4.3               MASS_7.3-51.4               zlibbioc_1.32.0             pkgbuild_1.0.6              plyr_1.8.4                  grid_3.6.1                  parallel_3.6.1              crayon_1.3.4               
[64] lattice_0.20-38             splines_3.6.1               ps_1.3.0                    pillar_1.4.2                fda_2.4.8                   corpcor_1.6.9               stats4_3.6.1                pkgload_1.0.2               XML_3.98-1.20               glue_1.3.1                  latticeExtra_0.6-28         data.table_1.12.6           remotes_2.1.0               RcppParallel_4.4.4          testthat_2.3.0              gtable_0.3.0                purrr_0.3.3                 clue_0.3-57                 assertthat_0.2.1            ks_1.11.6                   ggplot2_3.3.0              
[85] ConsensusClusterPlus_1.50.0 IDPmisc_1.1.19              pcaPP_1.9-73                tibble_2.1.3                memoise_1.1.0               flowViz_1.50.0              ellipse_0.4.1               cluster_2.1.0               CytoML_1.12.1               ellipsis_0.3.0
lmweber commented 4 years ago

Yes, it seems there were some changes made to the user interface for FlowSOM, so some of this code will no longer run without modification.

These two repositories you are commenting on are now 3-4 years old, so this is normal.

I do not have time to update these repositories, so instead I would suggest having a look at the latest FlowSOM vignette, where you can see the latest code for running FlowSOM. The vignette is available here or via the Bioconductor link I posted above.

Also please be mindful of your tone in these messages. Your phrasing "I too am getting this error when running your very own code" comes across as rude, even if that is not your intention. We provide these code repositories on a volunteer basis, as a resource for the community.

malcook commented 4 years ago

Great thanks for your reply, @lmweber, and for pointing out how my phrasing comes across. I see your point. Huge apologies. Really. I'm sorry.

I'll look more closely at the vignette for I am sure my experience is due to operator error in the face of changing interface to FlowSOM. If I learn something worth sharing, I'll share it back here.

In the meantime, thanks for your cytometry clustering comparison. Running through it has given me a quick (re) introduction to a number of issues at play in HD cytometry analysis.

lmweber commented 4 years ago

Great, no worries!

Yes good idea, if you find out something useful, it might also be useful to post it here to help others in the future.