[BioC] using beadarray to analyze data from iScan

[John Alexander]

Hi,
   I must say that I'm fairly new to microarrays and is my first attempt.
I have 2 chips with 6 heterozygous samples on one and wildtype 
on the other (poorly designed).The chip is MOUSEWG-6_V2.

I have the raw data which is the output from iScan and needs to be processed 
using processSwathData function and also the Final data - which is the 
summarised data from GenomeStudio.  I have all the necessary files- 
Swath_Grn.locs,.tif,Metrics,_beadTypeFile.txt,perBeadTypeFile.txt for analysis.

Running the processSwathData function with default values (I dont know how to 
find the value for swathOverlap parameter)

processSwathData(inputDir = dir1, outputDir =dirOp1 , twoColour=NULL, 
textstring="_perBeadFile.txt", segmentHeight = 326, segmentWidth = 397, 
swathOverlap = 81, fullOutput = FALSE, newTextString=".txt", verbose = FALSE)

Output...
Ist chip:
5665095021_A_1 
5665095021_A_2 
5665095021_B_1 

Error in if (all(txt[txtDups[i + 1], 3:4] == txt[txtDups[i], 3:4])) { : 
  missing value where TRUE/FALSE needed

2nd Chip :
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  scan() expected 'an integer', got '0.72'

I noticed that in 5665095021_A_1_perBeadFile.txt, in line it has only one 
entry (0.72) instead of 4. Is there a way to bypass this problem because I 
cannot read into the function readIllumina()

 On the other hand I am trying to proceed with the summarised Data 
from GenomeStudio. I donot have much information to perform analysis
 on this output iScanb using beadarray. 
Is there a way to club the summarised data from both the chips.
 I tried the combine function but it does not work. 

Any tutorials on this would be appreciated. 

Kind regards,
John.