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Question: Compensating using spillover function of flowCore
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gravatar for John Pura
6.6 years ago by
John Pura20
John Pura20 wrote:
Hello, I've been running into some issues in computing the spillover matrix using flowCore. I've searched the archives, and there seems to be someone else from 2 years ago who had this problem; however, I tried the suggested fixes to no avail, and I'm not sure if the original poster ever resolved the problem. Here is a brief description of my dataset: I have a flowSet with 10 experiments, the first of which is my unstained control fcs file. Experiments 2-10 correspond to FITC-A PE-A PE-Cy7-A V450-A APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A The following are the column names of each flowFrame: FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time I call the spillover function as follows: namepatt <- "FITC-A|PE-A|PE-Cy7-A|V450-A|APC-A|Alexa 700-A|QDot 655-A|APC-Cy7-A|Pac Orange-A" comp.mat <- spillover(compdat[,c(1,3,5:13)],unstained = sampleNames(compdat)[1], patt = namepatt,fsc = "FSC-A", ssc = "SSC-A",method = "median",useNormFilt = TRUE) Notice the useNormFilt = TRUE. I have set it to FALSE and also get the same error message: Error in .local(x, ...) : subscript out of bounds Does anyone know what is going on here? Help is much appreciated Thanks, John [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by John Pura20
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gravatar for John Pura
6.6 years ago by
John Pura20
John Pura20 wrote:
Thanks for the feedback, Dr. Finak. I've provided the outputs for sessionInfo(), summary(compdat), and traceback(). Here is the output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools grid splines stats graphics grDevices utils [8] datasets methods base other attached packages: [1] flowQ_1.14.1 latticeExtra_0.6-19 RColorBrewer_1.0-5 [4] parody_1.12.0 bioDist_1.26.0 KernSmooth_2.23-7 [7] outliers_0.14 flowMerge_2.2.0 foreach_1.3.2 [10] codetools_0.2-8 iterators_1.0.5 snow_0.3-8 [13] Rgraphviz_1.32.0 graph_1.32.0 flowType_1.0.0 [16] flowTrans_1.6.0 flowClust_2.12.1 ellipse_0.3-5 [19] mnormt_1.4-5 flowViz_1.18.0 lattice_0.20-0 [22] flowMeans_1.6.0 flowStats_1.12.0 cluster_1.14.1 [25] mvoutlier_1.9.4 robCompositions_1.5.0 car_2.0-12 [28] nnet_7.3-1 compositions_1.10-2 energy_1.4-0 [31] MASS_7.3-16 boot_1.3-4 tensorA_0.36 [34] rgl_0.92.798 fda_2.2.7 zoo_1.7-6 [37] flowCore_1.20.0 rrcov_1.3-01 pcaPP_1.9-45 [40] mvtnorm_0.9-9992 robustbase_0.8-0 Biobase_2.14.0 loaded via a namespace (and not attached): [1] annotate_1.32.1 AnnotationDbi_1.16.11 DBI_0.2-5 [4] feature_1.2.8 geneplotter_1.32.1 IRanges_1.12.5 [7] ks_1.8.5 RSQLite_0.11.1 sfsmisc_1.0-19 [10] stats4_2.14.1 xtable_1.6-0 Here is the output of summary(compdat) > summary(compdat) $`Compensation Controls_0_Unstained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22440 20030 -133.6 15 -67.32 -88.11 -90.09 -129.6 1st Qu. 73220 54480 38040.0 30560 160.40 59.40 12.87 68.4 Median 103100 78330 192800.0 142500 255.40 115.80 45.54 133.2 Mean 111300 85040 154900.0 117700 277.80 132.30 63.45 197.5 3rd Qu. 137600 109000 251500.0 178100 329.70 167.30 88.11 200.7 Max. 262100 255100 262100.0 256800 47470.00 18800.00 13190.00 51810.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -56.28 -57.96 -387.9 -115.10 -92.7 0.9 1st Qu. 127.70 10.08 194.4 -11.76 274.5 459.9 Median 615.70 34.44 472.5 14.28 454.5 932.0 Mean 620.90 40.98 510.9 18.88 553.3 943.6 3rd Qu. 915.80 60.48 731.7 42.00 604.8 1390.0 Max. 16950.00 6660.00 29000.0 3879.00 131300.0 2086.0 $`Compensation Controls_1_FITC Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 21500 20120 -187.1 50 -391.1 -182.20 -84.15 -122.4 1st Qu. 72140 53460 41700.0 33510 180.2 70.29 14.85 90.0 Median 113500 90580 175600.0 130700 266.3 121.80 50.49 156.1 Mean 119700 91690 149200.0 111600 2615.0 473.80 69.82 285.3 3rd Qu. 173500 130600 234000.0 166900 352.4 177.20 93.06 237.6 Max. 262100 255100 262100.0 256800 179500.0 228800.00 23330.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -186.5 -92.40 -370.8 -104.20 -181.8 67.7 1st Qu. 173.9 22.68 220.5 -5.04 302.4 444.6 Median 564.9 48.72 445.5 21.00 487.8 950.6 Mean 614.0 64.29 522.9 29.12 739.1 993.2 3rd Qu. 843.6 80.64 687.8 51.24 669.6 1515.0 Max. 32250.0 11370.00 34180.0 6395.00 262100.0 2051.0 $`Compensation Controls_2_PE Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22940 20020 127.7 182 -68.31 -105.90 -89.10 -108.90 1st Qu. 68660 50800 43150.0 34500 180.20 72.27 15.84 87.97 Median 113700 91500 173900.0 130400 252.40 123.80 50.49 148.00 Mean 119000 91440 150200.0 112000 439.40 602.40 89.98 354.50 3rd Qu. 172200 131000 230800.0 164500 323.70 177.20 93.06 215.10 Max. 262100 255100 262100.0 256800 262100.00 262100.00 63440.00 262100.00 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -37.8 -78.12 -297.9 -106.70 -77.4 2.3 1st Qu. 174.7 14.28 245.7 -7.56 296.1 589.0 Median 568.7 44.52 466.2 20.16 458.1 1244.0 Mean 658.3 82.72 595.4 36.42 729.6 1262.0 3rd Qu. 835.0 81.48 693.9 50.61 612.0 1905.0 Max. 127100.0 65180.00 190400.0 29760.00 262100.0 2608.0 $`Compensation Controls_3_PE-Cy7 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -2874000 20060 5497 4909 -40.59 -92.07 -293.00 -110.7 1st Qu. 75670 57080 53390 42090 184.10 77.22 95.04 90.9 Median 106000 82500 198800 148100 255.40 125.70 253.40 154.8 Mean 116000 89860 168900 129600 365.90 197.30 694.50 245.4 3rd Qu. 165100 126700 253800 182300 326.70 174.20 524.90 225.0 Max. 262100 255100 262100 256800 154400.00 90470.00 262100.00 130900.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -28.56 -57.12 -335.7 -107.50 -87.3 38.0 1st Qu. 197.40 15.12 272.7 -1.68 314.1 420.0 Median 655.60 37.80 531.0 28.56 473.4 936.5 Mean 716.30 57.11 650.4 134.70 660.3 964.9 3rd Qu. 932.40 63.00 763.2 62.16 617.4 1482.0 Max. 122700.00 32030.00 247200.0 122200.00 262100.0 2016.0 $`Compensation Controls_4_V450 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22690 20020 -91.08 13 -53.46 -104.00 -121.80 -130.5 1st Qu. 77500 58050 43490.00 34750 177.20 64.35 15.84 157.5 Median 103100 78780 198700.00 146500 254.40 114.80 50.49 252.0 Mean 110800 85190 161500.00 123200 274.10 124.70 60.86 851.9 3rd Qu. 133600 106100 253500.00 181400 327.70 161.40 92.07 376.2 Max. 262100 255100 262100.00 256800 12860.00 6253.00 3270.00 33160.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -42.84 -55.44 -327.6 -99.12 -78.3 0.1 1st Qu. 156.20 8.40 236.7 -11.76 383.4 463.5 Median 630.80 29.40 503.1 13.44 537.3 1136.0 Mean 655.60 32.99 548.6 16.26 773.1 1171.0 3rd Qu. 917.30 52.08 749.0 40.32 722.7 1816.0 Max. 37890.00 2163.00 45720.0 1352.00 34480.0 2549.0 $`Compensation Controls_5_APC Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Min. 20240 20020 5228 4612 -53.46 -126.70 -90.09 -139.5 -541.0 1st Qu. 70300 52930 37010 30020 151.50 50.49 12.87 74.7 279.5 Median 102300 78760 188400 140200 230.70 101.00 46.53 143.5 754.3 Mean 110700 84420 152400 115900 248.70 113.20 58.26 181.6 2726.0 3rd Qu. 141300 110400 243800 174800 300.00 149.50 87.12 214.2 1123.0 Max. 262100 255100 262100 256800 12960.00 6089.00 2752.00 19060.0 262100.0 Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -113.40 -419.4 -124.30 -124.2 884.8 1st Qu. 14.28 243.0 -10.92 246.6 1236.0 Median 52.08 528.8 20.16 408.6 1587.0 Mean 510.40 765.0 115.30 482.1 1593.0 3rd Qu. 97.44 794.7 57.96 562.7 1944.0 Max. 73160.00 37700.0 15620.00 27730.0 2321.0 $`Compensation Controls_6_Alexa 700 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -2622000 20020 141.6 120 -67.32 -121.80 -77.22 -121.5 1st Qu. 72730 54960 40080.0 32480 173.20 61.38 22.77 74.7 Median 102100 77940 198800.0 147400 251.50 110.90 61.38 139.5 Mean 109700 84430 160100.0 122300 278.50 126.00 74.92 171.4 3rd Qu. 135400 107500 254700.0 181500 322.70 160.40 102.00 209.7 Max. 262100 255100 262100.0 256800 63190.00 29600.00 15580.00 43060.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -55.44 -90.72 -389.7 -110.00 -101.7 0.1 1st Qu. 203.30 94.92 234.9 18.48 282.6 461.0 Median 665.30 157.90 506.2 60.48 444.6 956.8 Mean 695.40 702.00 573.8 213.50 524.1 974.9 3rd Qu. 932.40 259.60 760.7 125.20 594.9 1483.0 Max. 134000.00 153800.00 159500.0 93380.00 123600.0 2011.0 $`Compensation Controls_7_QDot 655 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22650 20040 -176.2 17 -47.52 -105.90 -82.17 -131.4 1st Qu. 57470 43840 45760.0 36230 166.30 60.39 17.82 71.1 Median 83440 62800 198700.0 144300 236.60 107.90 51.48 134.1 Mean 96230 73220 163700.0 123100 336.20 168.70 98.69 262.6 3rd Qu. 120200 94580 251500.0 177500 306.90 154.40 91.08 203.4 Max. 262100 255000 262100.0 256800 262100.00 172500.00 56410.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -71.4 -47.88 -641.7 -99.12 -73.8 81.7 1st Qu. 679.6 24.36 879.1 -9.24 269.1 859.6 Median 983.6 47.04 2632.0 15.12 411.3 2204.0 Mean 4198.0 175.30 23880.0 24.77 614.0 2265.0 3rd Qu. 1548.0 78.12 10840.0 43.68 552.6 3623.0 Max. 262100.0 60750.00 262100.0 7120.00 262100.0 4832.0 $`Compensation Controls_8_APC-Cy7 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -3196000 20040 5199 4744 -46.53 -101.00 -80.19 -208.8 1st Qu. 70120 52830 44540 35680 174.20 60.39 18.81 82.8 Median 94710 70700 206200 151400 246.50 108.90 53.46 146.7 Mean 104300 80270 167700 128600 348.30 161.90 120.60 294.3 3rd Qu. 126400 100600 262100 188700 316.80 158.40 97.02 219.6 Max. 262100 255100 262100 256800 220600.00 100300.00 86300.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -432.6 -56.28 -370.8 -239.40 -64.8 0.7 1st Qu. 254.3 10.92 271.8 10.92 285.3 445.3 Median 724.9 32.76 537.3 52.92 429.3 974.1 Mean 859.7 73.50 834.9 545.40 637.8 1017.0 3rd Qu. 1029.0 56.28 785.7 122.60 572.4 1563.0 Max. 262100.0 24640.00 262100.0 262100.00 262100.0 2164.0 $`Compensation Controls_9_Pac Orange Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Min. 22550 20060 5352 4647 -50.49 -94.05 -70.29 -122.4 -26.88 1st Qu. 73900 55310 44820 35960 174.20 61.38 11.88 85.5 162.10 Median 101600 77290 198400 147400 246.50 111.90 44.55 153.0 641.80 Mean 111700 85420 165000 126600 279.10 128.20 58.68 308.4 662.00 3rd Qu. 137100 108100 260100 185800 317.80 159.40 83.16 224.1 938.50 Max. 262100 255100 262100 256800 11950.00 7378.00 10690.00 197800.0 8495.00 Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -61.32 -493.2 -97.44 -64.8 0.5 1st Qu. 6.72 243.7 -11.76 306.0 299.4 Median 26.88 546.8 12.60 483.3 701.1 Mean 32.90 709.5 25.83 998.8 723.9 3rd Qu. 48.72 822.8 40.32 654.3 1133.0 Max. 2895.00 87860.0 12060.00 244400.0 1565.0 > print(compdat) A flowSet with 10 experiments. column names: FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time > summary(compdat) $`Compensation Controls_0_Unstained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22440 20030 -133.6 15 -67.32 -88.11 -90.09 -129.6 1st Qu. 73220 54480 38040.0 30560 160.40 59.40 12.87 68.4 Median 103100 78330 192800.0 142500 255.40 115.80 45.54 133.2 Mean 111300 85040 154900.0 117700 277.80 132.30 63.45 197.5 3rd Qu. 137600 109000 251500.0 178100 329.70 167.30 88.11 200.7 Max. 262100 255100 262100.0 256800 47470.00 18800.00 13190.00 51810.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -56.28 -57.96 -387.9 -115.10 -92.7 0.9 1st Qu. 127.70 10.08 194.4 -11.76 274.5 459.9 Median 615.70 34.44 472.5 14.28 454.5 932.0 Mean 620.90 40.98 510.9 18.88 553.3 943.6 3rd Qu. 915.80 60.48 731.7 42.00 604.8 1390.0 Max. 16950.00 6660.00 29000.0 3879.00 131300.0 2086.0 $`Compensation Controls_1_FITC Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 21500 20120 -187.1 50 -391.1 -182.20 -84.15 -122.4 1st Qu. 72140 53460 41700.0 33510 180.2 70.29 14.85 90.0 Median 113500 90580 175600.0 130700 266.3 121.80 50.49 156.1 Mean 119700 91690 149200.0 111600 2615.0 473.80 69.82 285.3 3rd Qu. 173500 130600 234000.0 166900 352.4 177.20 93.06 237.6 Max. 262100 255100 262100.0 256800 179500.0 228800.00 23330.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -186.5 -92.40 -370.8 -104.20 -181.8 67.7 1st Qu. 173.9 22.68 220.5 -5.04 302.4 444.6 Median 564.9 48.72 445.5 21.00 487.8 950.6 Mean 614.0 64.29 522.9 29.12 739.1 993.2 3rd Qu. 843.6 80.64 687.8 51.24 669.6 1515.0 Max. 32250.0 11370.00 34180.0 6395.00 262100.0 2051.0 $`Compensation Controls_2_PE Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22940 20020 127.7 182 -68.31 -105.90 -89.10 -108.90 1st Qu. 68660 50800 43150.0 34500 180.20 72.27 15.84 87.97 Median 113700 91500 173900.0 130400 252.40 123.80 50.49 148.00 Mean 119000 91440 150200.0 112000 439.40 602.40 89.98 354.50 3rd Qu. 172200 131000 230800.0 164500 323.70 177.20 93.06 215.10 Max. 262100 255100 262100.0 256800 262100.00 262100.00 63440.00 262100.00 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -37.8 -78.12 -297.9 -106.70 -77.4 2.3 1st Qu. 174.7 14.28 245.7 -7.56 296.1 589.0 Median 568.7 44.52 466.2 20.16 458.1 1244.0 Mean 658.3 82.72 595.4 36.42 729.6 1262.0 3rd Qu. 835.0 81.48 693.9 50.61 612.0 1905.0 Max. 127100.0 65180.00 190400.0 29760.00 262100.0 2608.0 $`Compensation Controls_3_PE-Cy7 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -2874000 20060 5497 4909 -40.59 -92.07 -293.00 -110.7 1st Qu. 75670 57080 53390 42090 184.10 77.22 95.04 90.9 Median 106000 82500 198800 148100 255.40 125.70 253.40 154.8 Mean 116000 89860 168900 129600 365.90 197.30 694.50 245.4 3rd Qu. 165100 126700 253800 182300 326.70 174.20 524.90 225.0 Max. 262100 255100 262100 256800 154400.00 90470.00 262100.00 130900.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -28.56 -57.12 -335.7 -107.50 -87.3 38.0 1st Qu. 197.40 15.12 272.7 -1.68 314.1 420.0 Median 655.60 37.80 531.0 28.56 473.4 936.5 Mean 716.30 57.11 650.4 134.70 660.3 964.9 3rd Qu. 932.40 63.00 763.2 62.16 617.4 1482.0 Max. 122700.00 32030.00 247200.0 122200.00 262100.0 2016.0 $`Compensation Controls_4_V450 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22690 20020 -91.08 13 -53.46 -104.00 -121.80 -130.5 1st Qu. 77500 58050 43490.00 34750 177.20 64.35 15.84 157.5 Median 103100 78780 198700.00 146500 254.40 114.80 50.49 252.0 Mean 110800 85190 161500.00 123200 274.10 124.70 60.86 851.9 3rd Qu. 133600 106100 253500.00 181400 327.70 161.40 92.07 376.2 Max. 262100 255100 262100.00 256800 12860.00 6253.00 3270.00 33160.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -42.84 -55.44 -327.6 -99.12 -78.3 0.1 1st Qu. 156.20 8.40 236.7 -11.76 383.4 463.5 Median 630.80 29.40 503.1 13.44 537.3 1136.0 Mean 655.60 32.99 548.6 16.26 773.1 1171.0 3rd Qu. 917.30 52.08 749.0 40.32 722.7 1816.0 Max. 37890.00 2163.00 45720.0 1352.00 34480.0 2549.0 $`Compensation Controls_5_APC Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Min. 20240 20020 5228 4612 -53.46 -126.70 -90.09 -139.5 -541.0 1st Qu. 70300 52930 37010 30020 151.50 50.49 12.87 74.7 279.5 Median 102300 78760 188400 140200 230.70 101.00 46.53 143.5 754.3 Mean 110700 84420 152400 115900 248.70 113.20 58.26 181.6 2726.0 3rd Qu. 141300 110400 243800 174800 300.00 149.50 87.12 214.2 1123.0 Max. 262100 255100 262100 256800 12960.00 6089.00 2752.00 19060.0 262100.0 Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -113.40 -419.4 -124.30 -124.2 884.8 1st Qu. 14.28 243.0 -10.92 246.6 1236.0 Median 52.08 528.8 20.16 408.6 1587.0 Mean 510.40 765.0 115.30 482.1 1593.0 3rd Qu. 97.44 794.7 57.96 562.7 1944.0 Max. 73160.00 37700.0 15620.00 27730.0 2321.0 $`Compensation Controls_6_Alexa 700 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -2622000 20020 141.6 120 -67.32 -121.80 -77.22 -121.5 1st Qu. 72730 54960 40080.0 32480 173.20 61.38 22.77 74.7 Median 102100 77940 198800.0 147400 251.50 110.90 61.38 139.5 Mean 109700 84430 160100.0 122300 278.50 126.00 74.92 171.4 3rd Qu. 135400 107500 254700.0 181500 322.70 160.40 102.00 209.7 Max. 262100 255100 262100.0 256800 63190.00 29600.00 15580.00 43060.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -55.44 -90.72 -389.7 -110.00 -101.7 0.1 1st Qu. 203.30 94.92 234.9 18.48 282.6 461.0 Median 665.30 157.90 506.2 60.48 444.6 956.8 Mean 695.40 702.00 573.8 213.50 524.1 974.9 3rd Qu. 932.40 259.60 760.7 125.20 594.9 1483.0 Max. 134000.00 153800.00 159500.0 93380.00 123600.0 2011.0 $`Compensation Controls_7_QDot 655 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. 22650 20040 -176.2 17 -47.52 -105.90 -82.17 -131.4 1st Qu. 57470 43840 45760.0 36230 166.30 60.39 17.82 71.1 Median 83440 62800 198700.0 144300 236.60 107.90 51.48 134.1 Mean 96230 73220 163700.0 123100 336.20 168.70 98.69 262.6 3rd Qu. 120200 94580 251500.0 177500 306.90 154.40 91.08 203.4 Max. 262100 255000 262100.0 256800 262100.00 172500.00 56410.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -71.4 -47.88 -641.7 -99.12 -73.8 81.7 1st Qu. 679.6 24.36 879.1 -9.24 269.1 859.6 Median 983.6 47.04 2632.0 15.12 411.3 2204.0 Mean 4198.0 175.30 23880.0 24.77 614.0 2265.0 3rd Qu. 1548.0 78.12 10840.0 43.68 552.6 3623.0 Max. 262100.0 60750.00 262100.0 7120.00 262100.0 4832.0 $`Compensation Controls_8_APC-Cy7 Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A Min. -3196000 20040 5199 4744 -46.53 -101.00 -80.19 -208.8 1st Qu. 70120 52830 44540 35680 174.20 60.39 18.81 82.8 Median 94710 70700 206200 151400 246.50 108.90 53.46 146.7 Mean 104300 80270 167700 128600 348.30 161.90 120.60 294.3 3rd Qu. 126400 100600 262100 188700 316.80 158.40 97.02 219.6 Max. 262100 255100 262100 256800 220600.00 100300.00 86300.00 262100.0 APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -432.6 -56.28 -370.8 -239.40 -64.8 0.7 1st Qu. 254.3 10.92 271.8 10.92 285.3 445.3 Median 724.9 32.76 537.3 52.92 429.3 974.1 Mean 859.7 73.50 834.9 545.40 637.8 1017.0 3rd Qu. 1029.0 56.28 785.7 122.60 572.4 1563.0 Max. 262100.0 24640.00 262100.0 262100.00 262100.0 2164.0 $`Compensation Controls_9_Pac Orange Stained Control.fcs` FSC-A FSC-H SSC-A SSC-H FITC-A PE-A PE-Cy7-A V450-A APC-A Min. 22550 20060 5352 4647 -50.49 -94.05 -70.29 -122.4 -26.88 1st Qu. 73900 55310 44820 35960 174.20 61.38 11.88 85.5 162.10 Median 101600 77290 198400 147400 246.50 111.90 44.55 153.0 641.80 Mean 111700 85420 165000 126600 279.10 128.20 58.68 308.4 662.00 3rd Qu. 137100 108100 260100 185800 317.80 159.40 83.16 224.1 938.50 Max. 262100 255100 262100 256800 11950.00 7378.00 10690.00 197800.0 8495.00 Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A Time Min. -61.32 -493.2 -97.44 -64.8 0.5 1st Qu. 6.72 243.7 -11.76 306.0 299.4 Median 26.88 546.8 12.60 483.3 701.1 Mean 32.90 709.5 25.83 998.8 723.9 3rd Qu. 48.72 822.8 40.32 654.3 1133.0 Max. 2895.00 87860.0 12060.00 244400.0 1565.0 Finally, here is the output of traceback(): 3: .local(x, ...) 2: spillover(compdat[, c(1, 3, 5:13)], unstained = sampleNames(compdat)[1], patt = namepatt, fsc = "FSC-A", ssc = "SSC-A", method = "median", useNormFilt = TRUE) 1: spillover(compdat[, c(1, 3, 5:13)], unstained = sampleNames(compdat)[1], patt = namepatt, fsc = "FSC-A", ssc = "SSC-A", method = "median", useNormFilt = TRUE) [[alternative HTML version deleted]]
ADD COMMENTlink written 6.6 years ago by John Pura20
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