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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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cytofkit_analyzedFCS files are not created properly #41

Open smanne07 opened 6 years ago

smanne07 commented 6 years ago

Hi, The fcs files created by cytofkit dont seem to have the right number of cells and also dont have the new columns like tsne_1 e.t.c.

This was not a problem when using previous version of cytofkit.

Can you please help solve this issue?

Best regards Sasi

`sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages: [1] cytofkit_1.12.0 plyr_1.8.4 ggplot2_2.2.1

loaded via a namespace (and not attached): [1] Rtsne_0.13 VGAM_1.0-5 colorspace_1.3-2
[4] RcppEigen_0.3.3.4.0 class_7.3-14 rio_0.5.10
[7] corpcor_1.6.9 XVector_0.20.0 GenomicRanges_1.32.3
[10] proxy_0.4-22 ggrepel_0.8.0 mvtnorm_1.0-8
[13] codetools_0.2-15 splines_3.5.0 doParallel_1.0.11
[16] robustbase_0.93-0 cluster_2.0.7-1 graph_1.58.0
[19] shiny_1.1.0 rrcov_1.4-4 compiler_3.5.0
[22] assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1
[25] later_0.7.2 htmltools_0.3.6 tools_3.5.0
[28] igraph_1.2.1 gtable_0.2.0 GenomeInfoDbData_1.1.0
[31] RANN_2.5.1 reshape2_1.4.3 ggthemes_3.5.0
[34] Rcpp_0.12.17 carData_3.0-1 Biobase_2.40.0
[37] cellranger_1.1.0 RJSONIO_1.3-0 nlme_3.1-137
[40] gdata_2.18.0 iterators_1.0.9 lmtest_0.9-36
[43] laeken_0.4.6 stringr_1.3.1 openxlsx_4.1.0
[46] mime_0.5 miniUI_0.1.1.1 gtools_3.5.0
[49] XML_3.98-1.11 DEoptimR_1.0-8 zlibbioc_1.26.0
[52] MASS_7.3-49 zoo_1.8-1 scales_0.5.0
[55] VIM_4.7.0 colourpicker_1.0 promises_1.0.1
[58] parallel_3.5.0 SummarizedExperiment_1.10.1 curl_3.2
[61] stringi_1.1.7 S4Vectors_0.18.3 pcaPP_1.9-73
[64] foreach_1.4.4 permute_0.9-4 e1071_1.6-8
[67] flowCore_1.46.1 destiny_2.10.2 TTR_0.23-3
[70] caTools_1.17.1 BiocGenerics_0.26.0 boot_1.3-20
[73] zip_1.0.0 BiocParallel_1.14.1 GenomeInfoDb_1.16.0
[76] rlang_0.2.1 pkgconfig_2.0.1 matrixStats_0.53.1
[79] bitops_1.0-6 lattice_0.20-35 htmlwidgets_1.2
[82] pdist_1.2 magrittr_1.5 R6_2.2.2
[85] IRanges_2.14.10 gplots_3.0.1 DelayedArray_0.6.0
[88] mgcv_1.8-23 pillar_1.2.3 haven_1.1.1
[91] foreign_0.8-70 xts_0.10-2 scatterplot3d_0.3-41
[94] abind_1.4-5 RCurl_1.95-4.10 sp_1.3-1
[97] nnet_7.3-12 FlowSOM_1.12.0 tibble_1.4.2
[100] tsne_0.1-3 car_3.0-0 shinyFiles_0.6.2
[103] KernSmooth_2.23-15 grid_3.5.0 readxl_1.1.0
[106] data.table_1.11.4 vegan_2.5-2 ConsensusClusterPlus_1.44.0 [109] forcats_0.3.0 vcd_1.4-4 digest_0.6.15
[112] xtable_1.8-2 httpuv_1.4.3 stats4_3.5.0
[115] munsell_0.4.3 smoother_1.1 tcltk_3.5.0 `

lpeters1 commented 6 years ago

Has there been any progress on this? I am having the same issue. It seems to be merging the files appropriately but my analyzed fcs does not contain any of the cytofkit analysis parameters when viewed in FlowJo v10.

I am using a Mac with High Sierra and R v 3.5.0

Thanks!

rajsajjath commented 5 years ago

Hi, I am also wondering if there will be an update to fix this issue soon (sorry if this is spammy). I started experiencing the exact same problem as of the most recent update.

Cytofkit-analyzed .fcs files do not load properly in FlowJo v10 (as described by the others on this thread), and do not load at all into FCS Express 6 due to the following error: "The data start and end do not match: DataStart=4593, DataEnd=19672, DataBlockWidth=15080, RowCount=130, BytesPerRow=88, ExpectedDataBlockSizeInBytes=11440, Difference From Expected=3640".

I am using a Mac with high Sierra and R v3.5.0.

Thank you, Raj

StarXian commented 5 years ago

Me too, Has there been any progress on this?

SamGG commented 5 years ago

Hi, Install latest version of flowCore (1.47.5) from github and report if the problem is still there.

install.packages("devtools")
devtools::install_github("RGLab/flowCore")
StarXian commented 5 years ago

Thank you so much ,but there is still a problem.

Downloading GitHub repo RGLab/flowCore@master from URL https://api.github.com/repos/RGLab/flowCore/zipball/master Installation failed: 404: Not Found (404)

SamGG commented 5 years ago

Oooops! I forget there is no master branch for flowCore. Try (verified): devtools::install_github("RGLab/flowCore", ref = "trunk")