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ParkerICI / premessa

R package for pre-processing of mass and flow cytometry data
GNU General Public License v3.0
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Error in normalizer_GUI() #34

Open hzhu48187 opened 4 years ago

hzhu48187 commented 4 years ago

Hello,

I'm new to Premessa, and I've been trying to use the normalizer_GUI() to do bead normalization but running into repeated issues with this error: image

I've triple checked that the fcs files I'm feeding in have the same number of channels and channel names, but I keep getting this error no matter which fcs files I feed in (even two fcs files from the same experiment).

Would you have any insight on this? This also seems to happen regardless of if I choose "Fluidigm" or "beta beads" as an option. Thank you so much!

pfgherardini commented 4 years ago

Can you please open a new R session an post the result of running the following commands:

library(shiny)
library(premessa)
sessionInfo()
MLTWhite commented 4 years ago

I have the same question. I opened a new comment because I have two questions. Thank you!

angel611 commented 4 years ago

I need help, I am having the same error when i run premessa_GUI.i have tried to put xcode but its still not working. Any help? Listening on http://127.0.0.1:6994 Warning: Error in [: incorrect number of dimensions 90: compute_bead_slopes 89: correct_data_channels 88: FUN 87: lapply 86: premessa::normalize_folder 73: observeEventHandler [/Library/Frameworks/R.framework/Versions/3.5/Resources/library/premessa/normalizer_shinyGUI/server.R#266] 2: shiny::runApp 1: premessa::normalizer_GUI

my session info is sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.15.6

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] stats graphics grDevices utils datasets methods base

other attached packages: [1] premessa_0.2.6 shiny_1.5.0

loaded via a namespace (and not attached): [1] reticulate_1.13 remotes_2.2.0 lattice_0.20-38 pcaPP_1.9-73
[5] testthat_2.3.2 usethis_1.6.3 htmltools_0.5.0 stats4_3.5.3
[9] yaml_2.2.1 flowCore_1.48.1 rlang_0.4.7 pkgbuild_1.1.0
[13] later_1.1.0.1 glue_1.4.2 withr_2.3.0 BiocGenerics_0.28.0 [17] rhandsontable_0.3.7 sessioninfo_1.1.1 matrixStats_0.56.0 robustbase_0.93-5
[21] umap_0.2.5.0 htmlwidgets_1.5.1 devtools_2.3.2 mvtnorm_1.1-0
[25] memoise_1.1.0 Biobase_2.42.0 callr_3.4.4 fastmap_1.0.1
[29] httpuv_1.5.4 ps_1.3.4 parallel_3.5.3 fansi_0.4.1
[33] DEoptimR_1.0-8 Rcpp_1.0.5 corpcor_1.6.9 xtable_1.8-4
[37] openssl_1.4.1 backports_1.1.10 promises_1.1.1 desc_1.2.0
[41] pkgload_1.1.0 graph_1.60.0 jsonlite_1.7.1 mime_0.9
[45] fs_1.5.0 RSpectra_0.16-0 askpass_1.1 digest_0.6.25
[49] processx_3.4.4 grid_3.5.3 rprojroot_1.3-2 cli_2.0.2
[53] tools_3.5.3 magrittr_1.5 crayon_1.3.4 rrcov_1.5-2
[57] MASS_7.3-51.1 ellipsis_0.3.1 Matrix_1.2-15 prettyunits_1.1.1
[61] assertthat_0.2.1 rstudioapi_0.11 R6_2.4.1 compiler_3.5.3

pfgherardini commented 4 years ago

Can you please share in a Box/Dropbox/Googl Drive folder a couple of FCS files that fail? I need them to be able to reproduce the error and investigate.

angel611 commented 4 years ago

CYTOF DATA https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg Kindly ,here is the data

On Wed, 7 Oct 2020 at 21:17, Pier Federico Gherardini < notifications@github.com> wrote:

Can you please share in a Box/Dropbox/Googl Drive folder a couple of FCS files that fail? I need them to be able to reproduce the error and investigate.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/34#issuecomment-705110390, or unsubscribe https://github.com/notifications/unsubscribe-auth/APLOONJTTZJCDBOP446A5GTSJSWFJANCNFSM4LQ2F2AQ .

pfgherardini commented 4 years ago

The link is not accessible. Can you please make it publicly accessible?

Thanks

pfgherardini commented 4 years ago

Pinging you again @angel611 and @hzhu48187 . I am happy to look into this issue but i need data to reproduce it

angel611 commented 4 years ago

This is the link to the data

https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg?usp=sharing

On Tue, 13 Oct 2020 at 21:02, Pier Federico Gherardini < notifications@github.com> wrote:

Pinging you again @angel611 https://github.com/angel611 and @hzhu48187 https://github.com/hzhu48187 . I am happy to look into this issue but i need data to reproduce it

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/34#issuecomment-707914047, or unsubscribe https://github.com/notifications/unsubscribe-auth/APLOONOGXL5QI5RZFLA63X3SKSI3RANCNFSM4LQ2F2AQ .

angel611 commented 4 years ago

https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg

ZdSonwa commented 3 years ago

Has this issue been resolved? I am experiencing a similar problem where the run freezes with this message

Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Some data values of 'Ir193Di' channel exceed its $PnR value 4096 and will be truncated! To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE' Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Some data values of 'Time' channel exceed its $PnR value 997 and will be truncated! To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE' Warning: Error in [: incorrect number of dimensions 90: compute_bead_slopes 89: correct_data_channels 88: FUN 87: lapply 86: premessa::normalize_folder 73: observeEventHandler [C:\Users\Zd. Sonwa\Documents\R\win-library\4.0\premessa\normalizer_shinyGUI/server.R#266] 2: shiny::runApp 1: normalizer_GUI

pfgherardini commented 3 years ago

I used the files @angel611 above provided for testing and I could not reproduce. Can you please try upgrading to the latest version of the flowCore package? On my system with the following sessionInfo() the files normalize correctly

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] flowCore_1.52.1 shiny_1.5.0     premessa_0.2.6 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          compiler_3.6.3      pillar_1.4.6        later_1.1.0.1       plyr_1.8.6          tools_3.6.3        
 [7] digest_0.6.25       jsonlite_1.7.1      lifecycle_0.2.0     tibble_3.0.4        gtable_0.3.0        pkgconfig_2.0.3    
[13] rlang_0.4.8         cli_2.0.2           rstudioapi_0.11     parallel_3.6.3      fastmap_1.0.1       dplyr_1.0.2        
[19] withr_2.2.0         generics_0.0.2      vctrs_0.3.4         tidyselect_1.1.0    stats4_3.6.3        grid_3.6.3         
[25] reshape_0.8.8       glue_1.4.2          Biobase_2.46.0      R6_2.4.1            fansi_0.4.1         sessioninfo_1.1.1  
[31] farver_2.0.3        purrr_0.3.4         ggplot2_3.3.2       magrittr_1.5        scales_1.1.1        promises_1.1.1     
[37] matrixStats_0.56.0  htmltools_0.5.0     ellipsis_0.3.1      BiocGenerics_0.32.0 assertthat_0.2.1    mime_0.9           
[43] xtable_1.8-4        colorspace_1.4-1    httpuv_1.5.4        labeling_0.3        munsell_0.5.0       crayon_1.3.4

@ZdSonwa do you have some other files I can test? I only need one that's failing

ZdSonwa commented 3 years ago

Here is a subset of the data I used which gave me that error. https://drive.google.com/drive/folders/19K4KifCkya2rW8pUxDY-KxCtObxdGshi?usp=sharing

ZdSonwa commented 3 years ago

This is the version I'm using package version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
Biobase 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
cytolib 2.0.3 2020-06-09 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
flowCore 2.0.1 2020-06-09 [1] Bioconductor
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
premessa 0.2.6 2020-09-15 [1] Github (ParkerICI/premessa@467d641)

ZdSonwa commented 3 years ago

This is the version I'm using package version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
Biobase 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
cytolib 2.0.3 2020-06-09 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
flowCore 2.0.1 2020-06-09 [1] Bioconductor
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
premessa 0.2.6 2020-09-15 [1] Github (ParkerICI/premessa@467d641)

pfgherardini commented 3 years ago

I have tried everything I could think of to reproduce this bug, but I couldn't. @ZdSonwa can you send me an email at

[AT] parkerici [DOT] org, so that we can schedule a zoom meeting and look at this together?
ZdSonwa commented 3 years ago

@pfgherardini the email doesn't seem complete, or do you mean your user name before@

pfgherardini commented 3 years ago

Yes that's what i meant [AT] parkerici [DOT] org

Ferfera2610 commented 3 years ago

Hello, I get the same error and I am also a Mac user. I was wondering if this bug comes for Mac users rather than windows users or it is for something else. Here is my session info: R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base

other attached packages: [1] shiny_1.6.0 premessa_0.2.6 devtools_2.3.2 usethis_2.0.0 BiocManager_1.30.10

loaded via a namespace (and not attached): [1] Rcpp_1.0.6 jquerylib_0.1.3 bslib_0.2.4 compiler_3.6.2 later_1.1.0.1 prettyunits_1.1.1
[7] remotes_2.2.0 tools_3.6.2 testthat_3.0.1 digest_0.6.27 pkgbuild_1.2.0 pkgload_1.1.0
[13] jsonlite_1.7.2 memoise_2.0.0 lifecycle_0.2.0 rlang_0.4.10 cli_2.3.0 rstudioapi_0.13
[19] yaml_2.2.1 parallel_3.6.2 curl_4.3 xfun_0.20 fastmap_1.1.0 knitr_1.31
[25] withr_2.4.1 htmlwidgets_1.5.3 sass_0.3.1 desc_1.2.0 fs_1.5.0 stats4_3.6.2
[31] rprojroot_2.0.2 Biobase_2.44.0 glue_1.4.2 R6_2.5.0 processx_3.4.5 sessioninfo_1.1.1
[37] callr_3.5.1 purrr_0.3.4 magrittr_2.0.1 matrixStats_0.58.0 BiocGenerics_0.30.0 ps_1.5.0
[43] promises_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1 assertthat_0.2.1 rhandsontable_0.3.7 flowCore_1.50.0
[49] mime_0.9 xtable_1.8-4 httpuv_1.5.5 cachem_1.0.1 crayon_1.4.0

Thanks! Faezeh

pfgherardini commented 3 years ago

I think I had already tried to reproduce on Mac but I couldn't. However I am happy to try again. @Ferfera2610 can you share some data with me that displays the problem?

Thanks

Federico

Ferfera2610 commented 3 years ago

Hello again, Here is the data. It is public available dataset that I am trying to regenerate their results. If it is not Mac issue, I would like to use it on my own dataset afterward. Thanks! Faezeh combined.fcs.zip

Ferfera2610 commented 3 years ago

I think I had already tried to reproduce on Mac but I couldn't. However I am happy to try again. @Ferfera2610 can you share some data with me that displays the problem?

Thanks

Federico

Hello, I tried my files on windows system and it worked properly. However, I cannot redo it anymore and now that I try it again (in windows) I receive this error: Error in [: incorrect number of dimensions 2: shiny::runApp 1: normalizer_GUI Do you know what might be the issue? I have deleted the normed folder that was created before too. Thanks! Faezeh