[BioC] Factor-related problem when creating new flowFrame

[Kipper Fletez-Brant]

Hi,

I am having trouble understanding what is going wrong.  I am trying to 
create a new flowFrame that is in every way identical to an old 
flowFrame, but with one additional, new parameter.  I am able to 
reproduce it using the GvHD dataset.

My issue is down there at the very end of my example code when I try to 
plot - somehow in the flowFrame creation process my new flowFrame is 
presumed to have a factor somewhere in it.  As a result, I cannot plot 
with my new flowFrame.

I discovered this problem in another context, in which the same 
factor-related problem came up during the call to estimateLogicle. I 
have absolutely no idea what is going on here, as calling str() doesn't 
show factors at all.

Any help would be appreciated,
Kipper Fletez-Brant

********* Begin Example Code ***********

library(flowCore)
library(flowViz)
library(grid)

## look at given flowFrame, try to plot
ff <- GvHD[[1]]
 > ff
flowFrame object 's5a01'
with 3420 cells and 8 observables:
      name              desc range minRange maxRange
$P1 FSC-H        FSC-Height  1024        0     1023
$P2 SSC-H        SSC-Height  1024        0     1023
$P3 FL1-H         CD15 FITC  1024        1    10000
$P4 FL2-H           CD45 PE  1024        1    10000
$P5 FL3-H        CD14 PerCP  1024        1    10000
$P6 FL2-A              <NA>  1024        0     1023
$P7 FL4-H          CD33 APC  1024        1    10000
$P8  Time Time (51.20 sec.)  1024        0     1023
153 keywords are stored in the 'description' slot

lgcl <- estimateLogicle(ff, parameters(ff)$name[c(1:7)])
ff.l <- transform(ff, lgcl)
 > str(exprs(ff.l))
  num [1:3420, 1:8] 4.06 3.77 3.64 3.71 3.6 ...
  - attr(*, "dimnames")=List of 2
   ..$ : NULL
   ..$ : Named chr [1:8] "FSC-H" "SSC-H" "FL1-H" "FL2-H" ...
   .. ..- attr(*, "names")= chr [1:8] "$P1N" "$P2N" "$P3N" "$P4N" ...

 > xyplot(`Time` ~ `FL4-H`, data=ff.l, alpha=0.5, smooth=FALSE, abs=TRUE)
Warning message:
In grid.Call.graphics(L_points, x$x, x$y, x$pch, x$size) :
   semi-transparency is not supported on this device: reported only once 
per page

## create new flowFrame, try to plot
a <- runif(length(exprs(ff)[,1]), 1, 1e4)
p <- parameters(ff)$data
p[9,] <- c("a", "a", 1024, 1, 1024)
ex <- cbind(exprs(ff), a)
ff2 <- new("flowFrame", exprs=ex, parameters=new("AnnotatedDataFrame", 
p), description=description(ff))

 > ff2
flowFrame object 's5a01'
with 3420 cells and 9 observables:
      name              desc range minRange maxRange
$P1 FSC-H        FSC-Height  1024        0     1023
$P2 SSC-H        SSC-Height  1024        0     1023
$P3 FL1-H         CD15 FITC  1024        1    10000
$P4 FL2-H           CD45 PE  1024        1    10000
$P5 FL3-H        CD14 PerCP  1024        1    10000
$P6 FL2-A              <NA>  1024        0     1023
$P7 FL4-H          CD33 APC  1024        1    10000
$P8  Time Time (51.20 sec.)  1024        0     1023
9       a                 a  1024        1     1024
153 keywords are stored in the 'description' slot

lgcl <- estimateLogicle(ff2, channels=parameters(ff2)$name[c(1:7)])
ff2.l <- transform(ff2, lgcl)
 > str(exprs(ff2.l))
  num [1:3420, 1:9] 6.77 6.48 6.35 6.42 6.31 ...
  - attr(*, "dimnames")=List of 2
   ..$ : NULL
   ..$ : chr [1:9] "FSC-H" "SSC-H" "FL1-H" "FL2-H" ...

 > xyplot(`Time` ~ `FL4-H`, data=ff2.l, alpha=0.5, smooth=FALSE, abs=TRUE)
Warning messages:
1: In Ops.factor(diff(tmp), 15) : / not meaningful for factors
2: In Ops.factor(tmp, c(-1, 1) * xd) : + not meaningful for factors
3: In Ops.factor(diff(tmp), 15) : / not meaningful for factors
4: In Ops.factor(tmp, c(-1, 1) * yd) : + not meaningful for factors
5: In Ops.factor(diff(tmp), 15) : / not meaningful for factors
6: In Ops.factor(tmp, c(-1, 1) * xd) : + not meaningful for factors
7: In Ops.factor(diff(tmp), 15) : / not meaningful for factors
8: In Ops.factor(tmp, c(-1, 1) * yd) : + not meaningful for factors


*********** Begin Session Info *************

 > sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=C                 LC_NUMERIC=C
  [3] LC_TIME=C                  LC_COLLATE=C
  [5] LC_MONETARY=C              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] grid      parallel  stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
  [1] flowViz_1.24.0       lattice_0.20-27      BiocInstaller_1.10.4
  [4] bit_1.1-11           changepoint_1.1.2    sfsmisc_1.0-25
  [7] flowCore_1.26.3      rrcov_1.3-4          pcaPP_1.9-49
[10] mvtnorm_0.9-9997     robustbase_0.90-2    Biobase_2.20.1
[13] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
  [1] DEoptimR_1.0-1      IDPmisc_1.1.17      KernSmooth_2.23-10
  [4] MASS_7.3-26         RColorBrewer_1.0-5  feature_1.2.10
  [7] graph_1.38.3        hexbin_1.26.3       ks_1.9.0
[10] latticeExtra_0.6-26 misc3d_0.8-4        rgl_0.93.996
[13] stats4_3.0.0        tools_3.0.0         zoo_1.7-11