[BioC] Beadarray import of iScan generated Illumina gene expression data

[Aliaksei Holik]

Dear members,

This is my first attempt to analyse a microarray and I would greatly 
appreciate some help.

The data was generated using MOUSEREF-8_V2 BeadChip by a third party. I 
provided RNA and got a CD back containing the data. Judging by the 
presence of Swath 1 and 2 files, arrays were scanned using iScan system, 
which prompts processing with processSwathData. As far as I understand, 
I need three types of files for this processing, including *swath*.tiff 
files, locs files and beadlevel.txt file. That's where the problem begins.

1) All images I received are in jpeg format. And even though Image 
header files contain the line <Compressed>false</Compressed> I'm not 
sure I'd be able to import the data into beadarray using these images.

2) I seem to miss .locs files. The files I've got in each chip's 
directory (I had 2 chips hybridised in total) are:
- various *.jpeg files including files containing swath in the name
- ChipName_Sample_Grn.idat files
- Effective.cfg file
- Several Metrics.txt file (it appears there were several rounds of 
scanning)
- Image header ChipName_Sample.xml files
- ChipName.sdf file
- ChipName_qc.txt file
- and finally 8 ChipName_Sample_perBeadFile.txt files of the following 
format:
Code    Grn    GrnX    GrnY
10008    102    621.3782    13898.54
10008    86    1875.903    23202.34
Etc...

My questions are:
- Do I need to wait for tiff files or can I use available jpegs?
- As far as I understand, locs files contain bead coordinates, but these 
seem to be present in beadlevel txt files. I wonder, therefore, if 
there's a workaround for the lack of locs files. Alternatively, can I 
import data straight into a LumiBatch object providing the format of my 
beadlevel txt file?
- Providing I go along with using beadarray for data import, how do I 
find swathOverlap parameter required by processSwathData. I found 
segment width and height in sdf file (only because they were 
conveniently the same size as in the command manual), but can't find 
anything remotely similar to the overlap parameter.

Your help is greatly appreciated.

Aliaksei.