Altering channel names does not merge panels from separate files

[dinomasic]

Hi,

I'm trying to clean multiple FCS data files for use with cytofkit. I've got samples analysed with the same markers but with slightly different channel numbers and names between fcs files. I've successfully used Premessa to delete additional channels but when I've edited channel names to match between panels, the result was that when I loaded the edited files into Premessa I've got two channels with the same name but no merging between the sample data, which means I can't use the FCS files together for downstream analysis.

I've included two images which show my problem, the first is before changing channel names, the second is after, showing the identical channel names but no merging between the panels.

Is it possible to use your program to merge these data files?

Thank you!

[pfgherardini]

Hi

Yes it should definitely be possible to do what you are describing, and this looks like it may be a bug in premessa. Can you share a Box / Dropbox folder with the original file as well as the files you got when you renamed the channels?

Thanks

Federico

[dinomasic]

Hi Federico,

Thanks for the reply here is a link to the files, I've not included all of the files I have as it's a large cohort but I've include a few files which show the differences I'm seeing.

I hope the link below is ok.

Thanks again,

Dino

https://drive.google.com/open?id=1YDq-5UBhjZPz6re8-9lVMXzvFGgljNRg

[pfgherardini]

Hi,

When I open the files in the Renamed folder with the panel editor everything looks ok to me (see attached screenshot).

Can you please type the following in a fresh R session, and post here the output you get?

library(premessa)
library(flowCore)
sessionInfo()

[dinomasic]

Hi.

Here are the results:

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] premessa_0.2.4 usethis_1.4.0 devtools_2.0.1 flowUtils_1.44.0 flowCore_1.46.2 cytofkit_1.12.0 plyr_1.8.4
[8] ggplot2_3.1.0

loaded via a namespace (and not attached): [1] backports_1.1.2 readxl_1.1.0 VGAM_1.0-6 RcppEigen_0.3.3.5.0
[5] igraph_1.2.2 ConsensusClusterPlus_1.44.0 lazyeval_0.2.1 sp_1.3-1
[9] splines_3.5.1 BiocParallel_1.14.2 GenomeInfoDb_1.16.0 digest_0.6.18
[13] foreach_1.4.4 htmltools_0.3.6 gdata_2.18.0 magrittr_1.5
[17] memoise_1.1.0 cluster_2.0.7-1 doParallel_1.0.14 remotes_2.0.2
[21] openxlsx_4.1.0 shinyFiles_0.7.2 matrixStats_0.54.0 xts_0.11-2
[25] pdist_1.2 prettyunits_1.0.2 colorspace_1.4-0 rrcov_1.4-7
[29] ggrepel_0.8.0 haven_2.0.0 tcltk_3.5.1 callr_3.0.0
[33] crayon_1.3.4 RCurl_1.95-4.11 jsonlite_1.5 graph_1.58.2
[37] glue_1.3.0 zoo_1.8-4 iterators_1.0.10 gtable_0.2.0
[41] zlibbioc_1.26.0 XVector_0.20.0 DelayedArray_0.6.6 car_3.0-2
[45] pkgbuild_1.0.2 BiocGenerics_0.26.0 DEoptimR_1.0-8 abind_1.4-5
[49] VIM_4.7.0 scales_1.0.0 mvtnorm_1.0-8 ggthemes_4.0.1
[53] miniUI_0.1.1.1 Rcpp_1.0.0 xtable_1.8-3 laeken_0.4.6
[57] foreign_0.8-71 proxy_0.4-22 FlowSOM_1.12.0 stats4_3.5.1
[61] tsne_0.1-3 vcd_1.4-4 htmlwidgets_1.3 gplots_3.0.1
[65] pkgconfig_2.0.2 XML_3.98-1.16 nnet_7.3-12 rlang_0.3.0.1
[69] reshape2_1.4.3 later_0.7.5 munsell_0.5.0 cellranger_1.1.0
[73] tools_3.5.1 cli_1.0.1 stringr_1.3.1 processx_3.2.0
[77] fs_1.2.6 zip_1.0.0 robustbase_0.93-3 caTools_1.17.1.1
[81] purrr_0.2.5 RANN_2.6 nlme_3.1-137 mime_0.6
[85] compiler_3.5.1 rstudioapi_0.8 curl_3.2 e1071_1.7-0
[89] smoother_1.1 tibble_1.4.2 pcaPP_1.9-73 stringi_1.2.4
[93] ps_1.2.1 desc_1.2.0 forcats_0.3.0 lattice_0.20-38
[97] Matrix_1.2-15 vegan_2.5-3 permute_0.9-4 pillar_1.3.0
[101] RUnit_0.4.32 lmtest_0.9-36 data.table_1.11.8 bitops_1.0-6
[105] corpcor_1.6.9 httpuv_1.4.5 GenomicRanges_1.32.7 R6_2.3.0
[109] promises_1.0.1 KernSmooth_2.23-15 rio_0.5.16 IRanges_2.14.12
[113] sessioninfo_1.1.1 codetools_0.2-15 boot_1.3-20 colourpicker_1.0
[117] MASS_7.3-51.1 gtools_3.8.1 assertthat_0.2.0 pkgload_1.0.2
[121] destiny_2.10.2 SummarizedExperiment_1.10.1 rprojroot_1.3-2 withr_2.1.2
[125] S4Vectors_0.18.3 GenomeInfoDbData_1.1.0 mgcv_1.8-26 parallel_3.5.1
[129] hms_0.4.2 grid_3.5.1 class_7.3-14 carData_3.0-2
[133] Rtsne_0.15 TTR_0.23-4 scatterplot3d_0.3-41 Biobase_2.40.0
[137] shiny_1.2.0 base64enc_0.1-3

[dinomasic]

Hi Federico,

I've just repeated the analysis and it looks like its worked this time.

[pfgherardini]

Ok. That's weird but glad it's solved now. I am gonna close the issue. Please reopen it if the problem persists