[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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