Dear guys, I am trying to get a compensation matrix from FC data (1 unstained and 4 single stained tubes) using spillover, but got stuck at that point.
Here is my little piece of code:
library(flowCore)
comp.files = list.files("~/Documentos/26-2-16-s100/395/compdata/", all.files = T, full.names = TRUE)#Read full directory
comp.fs <- read.flowSet(comp.files[3:7], transformation = F, alter.names = T)#[3:25])#trim off 2 first rows /. and /..
comp.fs <- comp.fs[, 3:30]# remove time fields
comp.fs <- comp.fs[ , c(2,5,10,13,16,19, 25)]#discard unused channels
comp.mat <- spillover(comp.fs, unstained = comp.fs[1], fsc = "FS.Lin", ssc = "SS.Lin", method = "median", stain_match = c("intensity", "ordered", "regexpr"),
useNormFilt = T, pregate = F, plot = T)
When sourced, I got this error:
Error in match(unstained, sampleNames(x)) : 'match' requires vectorial arguments
Now, here we have further details of my set and stuff:
> traceback() 8: match(unstained, sampleNames(x)) 7: .local(x, ...) 6: spillover(comp.fs, unstained = comp.fs[1], fsc = "FS.Lin", ssc = "SS.Lin", method = "median", stain_match = c("intensity", "ordered", "regexpr"), useNormFilt = T, pregate = F, plot = T) 5: spillover(comp.fs, unstained = comp.fs[1], fsc = "FS.Lin", ssc = "SS.Lin", method = "median", stain_match = c("intensity", "ordered", "regexpr"), useNormFilt = T, pregate = F, plot = T) at citom2.R#70 4: eval(expr, envir, enclos) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source("~/Documentos/citom/citom2.R", echo = TRUE)
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> comp.fs A flowSet with 5 experiments. column names: FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log --------------------------------------------------------------------------------- > summary (comp.fs) $`395us.fcs` FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log Min. 3132 10 0 0 0.00 0 0 1st Qu. 11810 5426 4784 5842 0.00 0 0 Median 12950 7313 7176 8482 0.00 5569 0 Mean 13100 8402 7087 8204 52.94 5641 2028 3rd Qu. 14300 10170 9453 10730 0.00 9411 133 Max. 45790 65540 33390 34480 18120.00 29840 42300 $FL.1.fcs FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log Min. 3105 13 0 0 0.0 0.0 0 1st Qu. 11940 5676 7789 6999 0.0 858.8 0 Median 13110 7670 10020 9571 0.0 6449.0 0 Mean 13270 9122 10860 9834 329.9 6344.0 2025 3rd Qu. 14510 10720 12480 11910 0.0 10130.0 1817 Max. 51230 65540 65530 63240 40900.0 50530.0 40220 $FL.2.fcs FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log Min. 3094 10 0 0 0.0 0 0 1st Qu. 11780 5544 4842 6387 0.0 2175 0 Median 12960 7423 7204 8967 0.0 7149 0 Mean 13150 8516 7135 8809 164.7 6859 1682 3rd Qu. 14330 10180 9444 11200 0.0 10660 0 Max. 61120 65540 51480 55280 39720.0 52080 38470 $FL.4.fcs FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log Min. 3040 10 0 0 0.0 0 0 1st Qu. 11530 5532 5011 6108 0.0 14990 3168 Median 12720 7492 7366 8721 0.0 18440 8018 Mean 12870 8734 7309 8479 103.1 18210 7608 3rd Qu. 14120 10420 9619 10970 0.0 21770 11380 Max. 51610 65540 42820 44260 28990.0 63660 62950 $FL.8.fcs FS.Lin SS.Lin FL.1.Log FL.2.Log FL.3.Log FL.4.Log FL.8.Log Min. 3090 10 0 0 0.00 0.0 0 1st Qu. 11890 5555 5089 6064 0.00 246.5 5452 Median 13090 7523 7398 8703 0.00 5926.0 10110 Mean 13230 8711 7344 8428 73.05 6037.0 9961 3rd Qu. 14480 10480 9620 10920 0.00 9713.0 13560 Max. 42020 65540 40000 41220 26260.00 43430.0 65530
--------------------------------------------------------------------------------- > sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10 locale: [1] LC_CTYPE=es_UY.UTF-8 LC_NUMERIC=C LC_TIME=es_UY.UTF-8 LC_COLLATE=es_UY.UTF-8 LC_MONETARY=es_UY.UTF-8 [6] LC_MESSAGES=es_UY.UTF-8 LC_PAPER=es_UY.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_UY.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] flowViz_1.34.0 lattice_0.20-33 flowDensity_1.4.0 flowCore_1.37.13 loaded via a namespace (and not attached): [1] GEOmap_2.3-8 pcaPP_1.9-60 Rcpp_0.12.3 MBA_0.0-8 nloptr_1.0.4 DEoptimR_1.0-4 [7] RColorBrewer_1.1-2 RSEIS_3.5-2 bitops_1.0-6 tools_3.2.3 lme4_1.1-10 nlme_3.1-125 [13] mgcv_1.8-10 RPMG_2.2-1 Matrix_1.2-3 graph_1.48.0 parallel_3.2.3 SparseM_1.7 [19] mvtnorm_1.0-5 spam_1.3-0 hexbin_1.27.1 cluster_2.0.3 MatrixModels_0.4-1 gtools_3.5.0 [25] IDPmisc_1.1.17 caTools_1.17.1 fields_8.3-6 RFOC_3.3-3 maps_3.1.0 nnet_7.3-11 [31] stats4_3.2.3 grid_3.2.3 robustbase_0.92-5 Biobase_2.30.0 rrcov_1.3-11 sp_1.2-2 [37] minqa_1.2.4 gdata_2.17.0 latticeExtra_0.6-26 car_2.1-1 corpcor_1.6.8 splines_3.2.3 [43] gplots_2.17.0 splancs_2.01-38 matrixStats_0.50.1 MASS_7.3-45 BiocGenerics_0.16.1 pbkrtest_0.4-6 [49] Rwave_2.4 quantreg_5.21 KernSmooth_2.23-15
Thank you very much for your help!
D