[BioC] beadarray package: problem with bead level data

[Krys Kelly]

I am having a problem with bead level data.

I have .txt files containing over 900,000 lines with four columns: Code,
Grn, GrnX and GrnY. 

The image files are .jpg rather than .tif. I have converted the .jpg images
to .tif using Adobe Photoshop (trying several of the conversion options).
They always look like a beautiful starry night sky, which I think is what is
expected.

However, the data in the beadarray object is not what I expected.  In G
there are a lot of negative and zero values and all the Gb values are zero.

On Wednesday, I downloaded the latest version of R, beadarray and the
packages it depends on (see sessionInfo below).

Is the problem with my .tif files, or is there a problem of incompatibility
with the new version of R and the dependencies, or something else?

Thanks for any light you can shed.

Krys

Here is my code and output:

> BLData <- readIllumina(textType=".txt")
Found 2 arrays 
Reading pixels of 1863191039_A_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
> an <- arrayNames(BLData)
> summary(BLData at beadData[[an[1]]]$G)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-9547.0     0.0     0.0   371.1   267.5 30110.0 
> summary(BLData at beadData[[an[1]]]$Gb)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      0       0       0       0       0       0 
> 
> lengthG <- length(BLData at beadData[[an[1]]]$G)
> lengthG
[1] 904963
> myNegatives <-
length(BLData at beadData[[an[1]]]$G[BLData at beadData[[an[1]]]$G<0])
> myNegatives
[1] 169302
> myZeros <-
length(BLData at beadData[[an[1]]]$G[BLData at beadData[[an[1]]]$G==0])
> myZeros
[1] 360331
> myPositives <-
length(BLData at beadData[[an[1]]]$G[BLData at beadData[[an[1]]]$G>0])
> myPositives
[1] 375330
>

Here is my sessionInfo:

R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] "grid"      "tools"     "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "methods"   "base"     

other attached packages:
   beadarray beadarraySNP  quantsmooth      lodplot     quantreg
SparseM 
     "1.4.0"      "1.2.0"      "1.2.0"        "1.1"       "4.08"
"0.73" 
        affy       affyio  geneplotter      lattice     annotate
Biobase 
    "1.14.2"      "1.4.1"     "1.14.0"    "0.15-11"     "1.14.1"
"1.14.1" 
       limma 
    "2.10.5"


Dr Krystyna A Kelly (Krys)
 
Department of Pathology
University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
Tel: 01223 333331

and

MRC Biostatistics Unit
Institute of Public Health, Robinson Way, Cambridge CB2 0SR
Tel: 01223 767408

Email: kak28 at cam.ac.uk