Channel description gone after processing

[DMrdjen]

Hi! I just ran the normalization and bead removal and ended up with nicely normalized fcs files without beads but I lost the description of each channel. It looks like Nd145Di::Nd145Di instead. Just wondering if that's supposed to happen? I'd much rather have the descriptor than the channel name at the end...The descriptor seems to be lost completely.

[pfgherardini]

Hi. No that's not supposed to happen. Can you please share with me one representative file so that I can reproduce the problem and solve it? Thanks!

[DMrdjen]

I shared it with you on Community Cytobank. Thanks for the help! -Dunja

[pfgherardini]

Hi Dunja

I cannot reproduce this with the latest version of the package. Everything seems to work correctly here. Can you please share the output of running the following commands in your R session

library(premessa)
sessionInfo()

The latest version of the package is 0.1.7. Please reinstall it if you are running an earlier version, and let me know if the problem persists.

[DMrdjen]

I’m running version 0.1.7. Here’s the output:

library(premessa) sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4

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_0.1.7 devtools_1.13.5

loaded via a namespace (and not attached): [1] httr_1.3.1 compiler_3.5.0 R6_2.2.2 tools_3.5.0 withr_2.1.2 curl_3.2 memoise_1.1.0 [8] git2r_0.21.0 digest_0.6.15

-Dunja

---

Dunja Mrdjen, Ph.D. Postdoctoral researcher Bendall and Montine labs Department of Pathology Stanford University mrdjend@stanford.edu

On Jun 1, 2018, at 2:13 PM, Pier Federico Gherardini notifications@github.com wrote:

Hi Dunja

I cannot reproduce this with the latest version of the package. Everything seems to work correctly here. Can you please share the output of running the following commands in your R session

library(premessa) sessionInfo() The latest version of the package is 0.1.7. Please reinstall it if you are running an earlier version, and let me know if the problem persists.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/16#issuecomment-394010653, or mute the thread https://github.com/notifications/unsubscribe-auth/ATLIvWjHhJKMrPMSAcH9Xa_OiMAbX4N9ks5t4a5_gaJpZM4UUGxf.

[pfgherardini]

That's really weird. Can you tell me what version of flowCore you are using by running the following

library(flowCore)
sessionInfo()

Thanks

[DMrdjen]

Sure.

library(flowCore) sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4

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] flowCore_1.46.1 shiny_1.1.0 premessa_0.1.7 devtools_1.13.5

loaded via a namespace (and not attached): [1] pcaPP_1.9-73 Rcpp_0.12.17 pillar_1.2.3 plyr_1.8.4 compiler_3.5.0
[6] DEoptimR_1.0-8 later_0.7.2 git2r_0.21.0 tools_3.5.0 digest_0.6.15
[11] tibble_1.4.2 gtable_0.2.0 jsonlite_1.5 memoise_1.1.0 lattice_0.20-35
[16] rlang_0.2.1 graph_1.58.0 curl_3.2 parallel_3.5.0 mvtnorm_1.0-7
[21] withr_2.1.2 httr_1.3.1 cluster_2.0.7-1 stats4_3.5.0 grid_3.5.0
[26] reshape_0.8.7 robustbase_0.93-0 Biobase_2.40.0 R6_2.2.2 rrcov_1.4-4
[31] ggplot2_2.2.1 corpcor_1.6.9 magrittr_1.5 scales_0.5.0 promises_1.0.1
[36] matrixStats_0.53.1 htmltools_0.3.6 BiocGenerics_0.26.0 colorspace_1.3-2 mime_0.5
[41] xtable_1.8-2 httpuv_1.4.3 labeling_0.3 lazyeval_0.2.1 munsell_0.4.3

On Jun 1, 2018, at 5:46 PM, Pier Federico Gherardini notifications@github.com wrote:

That's really weird. Can you tell me what version of flowCore you are using by running the following

library(flowCore) sessionInfo() Thanks

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/16#issuecomment-394043474, or mute the thread https://github.com/notifications/unsubscribe-auth/ATLIvUHOLd_swcQ3YoII8EL_uDq96yqyks5t4eBQgaJpZM4UUGxf.

[pfgherardini]

Hi

I can confirm that this is due to the latest version of flowCore. I am investigating a fix

Federico

[pfgherardini]

Should be fixed in the latest version. Thanks for reporting and let me know if you have more issues

[DMrdjen]

Yes it’s working perfectly now, thanks so much for your help!

Dunja

On Jun 4, 2018, at 12:17 PM, Pier Federico Gherardini notifications@github.com wrote:

Should be fixed in the latest version. Thanks for reporting and let me know if you have more issues

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/16#issuecomment-394467240, or mute the thread https://github.com/notifications/unsubscribe-auth/ATLIvTmq9wBT1c-xQ9VeyVv_xZm7MKDUks5t5Ye7gaJpZM4UUGxf.

[DMrdjen]

Hi Federico,

I’m having another issue with Permessa. With specific fcs files I get this problem (see screenshot). Not sure why as these files should be the same as any other. Any ideas? I can upload them to Cytobank if you want to take a look.

Dunja

---

Dunja Mrdjen, Ph.D. Postdoctoral fellow Bendall and Montine labs Department of Pathology Stanford University mrdjend@stanford.edu

On Jun 4, 2018, at 12:17 PM, Pier Federico Gherardini notifications@github.com wrote:

Should be fixed in the latest version. Thanks for reporting and let me know if you have more issues

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ParkerICI/premessa/issues/16#issuecomment-394467240, or mute the thread https://github.com/notifications/unsubscribe-auth/ATLIvTmq9wBT1c-xQ9VeyVv_xZm7MKDUks5t5Ye7gaJpZM4UUGxf.

[DMrdjen]

[DMrdjen]

Hi again, I just realized this is because I don't have the Iridium 193, 194 channels in my panel...

[pfgherardini]

Yes, that would definitely cause those plots to fail

[DMrdjen]

Yeah :-) I don't alway use Iridium, so it's worth noting that one should always have the channel open even though there's no marker in there. I just added fake channels now since I had some others free, I could replace them in the panel editor.