[BioC] Illumina beadlevel expression data

[Ina Hoeschele]

Hi,
   I am new to the analysis of Illumina beadlevel expression data. I 
have data from a collaborator and have started to work with the data on 
the first Beadchip (with 12 arrays or strips).  These are single channel 
data. I am using the beadarray package.  I read the data in as follows:
BLData <- 
readIllumina(textType=".txt",useImages=TRUE,singleChannel=TRUE,imageManipulation="sharpen",
backgroundSize=17,storeXY=TRUE,metrics=FALSE,backgroundMethod="none",offset=0,normalizeMethod="none")
Note: above I'm doing NO background correction and note that I use 
backgroundSize=17.

Then I looked at the data:

an <- arrayNames(BLData)
BLData at beadData[[an[1]]]$G[1:10]
 [1]  0.0000000  2.5249867 -0.0359710  0.0000000  0.0000000 -6.8111267
 [7]  0.0000000 77.2345222 -0.8237067 -0.2324444
BLData at beadData[[an[1]]]$Gb[1:10]
 [1] 0 0 0 0 0 0 0 0 0 0

so I get quite a few G intensities that are zero and ALL of my 
background intensities are zero - why is that ?????

Then I created BLData with backgroundSize=4 and backgroundSize=40 (not 
knowing what value I should be using ?????). For backgroundSize=4, I 
find that
BLData at beadData[[an[1]]]$Gb[1:100]
  [1] -1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0
 [26]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  2  0  
0  0  0
 [51]  0  0 24  2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0
 [76]  0  0  0  0  0  0  0  0  0  0 19  0  0  0  0  0  0  0  0  0  0  0  
0  0  0
so now I still have many zero Gb values, but also some nonzero ones and 
even negative (-1)???
But when I use backgroundSize=40, then R crashes (repeatedly).

And when I create BLData with backgroundMethod="minimum" and 
backgroundSize=17, then I find the following G intensities:
BLData at beadData[[an[1]]]$G[1:10]
 [1] 2.425286e-12 2.524987e+00 2.425286e-12 2.425286e-12 2.425286e-12 
2.425286e-12 2.425286e-12 7.723452e+01 2.425286e-12
[10] 2.425286e-12

These G and Gb values all look suspect to me - can someone please help?

Many thanks, Ina