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Question: iFlow error messages
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gravatar for Gabriel Nathan Kaufman, Mr
5.7 years ago by
Canada
When I try to open some FCS files using iFlow, I get several strange error messages, and I am ultimately unable to open the files.... In iFlow, I get a pop-up box that says "Warning: 'signed = FALSE' is only valid for integers of sizes 1 and 2." In the R console, there are some warnings about RGtk2 'method' being deprecated - how can I clear this? When I try to open the FCS file directly in R using the underlying flowCore function read.FCS, I receive the same type of error message as from the iFlow GUI, but the file reads in properly into R. Why is the error message appearing, and why doesn't iFlow allow me to do the same thing, instead refusing to parse the file? [The FCS files are version 3.0 generated by FACSDiva 6.1.3; samples were acquired on a BD LSR II flow cytometer.] I copy the R console output below with session information at the end. --------------------------------------------- > library(iFlow) Loading required package: flowCore Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: rrcov Loading required package: robustbase Loading required package: pcaPP Loading required package: mvtnorm Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Attaching package: ?flowCore? The following object(s) are masked from ?package:stats?: filter Loading required package: flowViz Loading required package: lattice KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Loading required package: flowStats Loading required package: fda Loading required package: splines Loading required package: zoo Attaching package: ?zoo? The following object(s) are masked from ?package:base?: as.Date, as.Date.numeric Loading required package: mvoutlier Loading required package: compositions Loading required package: rgl Loading required package: tensorA Attaching package: ?tensorA? The following object(s) are masked from ?package:base?: norm Loading required package: energy Loading required package: boot Attaching package: ?boot? The following object(s) are masked from ?package:fda?: melanoma The following object(s) are masked from ?package:lattice?: melanoma The following object(s) are masked from ?package:robustbase?: salinity Loading required package: MASS Welcome to compositions, a package for compositional data analysis. Find an intro with "? compositions" Attaching package: ?compositions? The following object(s) are masked from ?package:flowCore?: normalize The following object(s) are masked from ?package:stats?: cor, cov, dist, var The following object(s) are masked from ?package:base?: %*%, scale, scale.default Loading required package: robCompositions Loading required package: car Loading required package: nnet Attaching package: ?car? The following object(s) are masked from ?package:boot?: logit -------- for references have a look at citation('robCompositions') -------- Attaching package: ?robCompositions? The following object(s) are masked from ?package:compositions?: alr, clr, ilr Loading required package: cluster Warning messages: 1: replacing previous import ?.__C__character? when loading ?methods? 2: 'method' is deprecated. Use ''gtk-enable-tooltips' property on GtkSettings' instead. See help("Deprecated") and help("RGtk2-deprecated"). Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSetFont: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSetFontSize: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSetTextMatrix: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSaveGState: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSetCompositeOperation: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextFillRects: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextRestoreGState: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextSetRGBFillColor: invalid context 0x0 Feb 8 15:48:31 golem.meakins.mcgill.ca R[403] <error>: CGContextShowGlyphsAtPoint: invalid context 0x0 > read.FCS("/Users/kaufman_home/Documents/Mazer lab files/data/Notch- Notch ligand phenotyping/Lung-DCs_OVA-HSA_1.fcs") flowFrame object '95d31115-ad3c-4c61-9685-c40b678950a7' with 10000 cells and 10 observables: name desc range minRange maxRange $P1 FSC-A <na> 262144 0.00 262143 $P2 SSC-A <na> 262144 0.00 262143 $P3 Alexa Fluor 488-A Dll1 262144 -43.68 262143 $P4 PE-A Jag1 262144 -105.84 262143 $P5 PerCP-A PE/Cy5 Jag2 262144 -111.00 262143 $P6 PE-Cy7-A F4/80 262144 -111.00 262143 $P7 Pacific Blue-A CD11c 262144 -53.82 262143 $P8 APC-A Dll4 262144 -111.00 262143 $P9 APC-Cy7-A CD11b 262144 -111.00 262143 $P10 Time <na> 262144 0.00 262143 171 keywords are stored in the 'description' slot Warning message: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] iFlow_2.6.0 flowStats_1.12.0 cluster_1.14.1 mvoutlier_1.9.4 [5] robCompositions_1.5.0 car_2.0-12 nnet_7.3-1 compositions_1.10-2 [9] energy_1.4-0 MASS_7.3-16 boot_1.3-4 tensorA_0.36 [13] rgl_0.92.798 fda_2.2.7 zoo_1.7-6 flowViz_1.18.0 [17] lattice_0.20-0 flowCore_1.20.0 rrcov_1.3-01 pcaPP_1.9-45 [21] mvtnorm_0.9-9992 robustbase_0.8-0 Biobase_2.14.0 loaded via a namespace (and not attached): [1] cairoDevice_2.19 feature_1.2.8 graph_1.32.0 grid_2.14.1 [5] KernSmooth_2.23-7 ks_1.8.5 latticeExtra_0.6-19 RColorBrewer_1.0-5 [9] RGtk2_2.20.21 stats4_2.14.1 tools_2.14.1 -------------------------------------------------------- Thank you in advance for your help. Gabriel Kaufman Meakins-Christie Laboratories McGill University Health Centre
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