[BioC] iFlow error messages
Gabriel Kaufman
gabriel.kaufman at mail.mcgill.ca
Wed Feb 8 22:53:24 CET 2012
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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