Hi Aliaksei,

I'm afraid it isn't appropriate to use the jpeg images.  As far as I'm
aware the jpegs produced by the Illumina scanner are always compressed, so
it's impossible to reproduce the tiff images that the intensities are
calculated from. Moreover, although the ordering of the beads on the array
grid won't have changed, the positions of the beads within the image will
almost certainly be different.  You can probably verify this by looking in
the two perBeadFile.txt files that were created for an array from the two
scans.  I'd expect you to see the same number of beads with each ID, and in
the same order, but with slightly different coordinate pairs.  Given
this, even if you could recreate the images from the first scan, it
wouldn't be appropriate to use them in combination with the coordinates of
the second.

If you're worried about the effects of rescanning, as a first test I would
read the two perBeadFile.txt files from the two scans and compare the
intensity values.  Don't worry about trying to split them into swaths for
this, as the ordering should be consistent between the two files.  If they
look similar then I'd simply use the second scan.  If the impact of the
rescanning looks large then you can use the processSwathData() function in
beadarray to split the files from the second scan and then, based on the
files that generates, go back and split the files from the first scan.
 That'll be quite a lot more work though, so hopefully the second scan is
fine.

I hope that helps,

Mike Smith

On Mon, Dec 19, 2011 at 12:54 PM, Aliaksei Holik <salvador@bio.bsu.by>wrote:

> Dear list members,
>
> Hopefully, this will be a straightforward question. I had my samples
> analysed on Illumina beadchip by university services using iScan. When I
> received the data all images were in jpeg format and there were no locs
> files, I assume due to compressed image format. After some discussion with
> the services my chips were re-scanned producing tiff images and appropriate
> locs files. However, there was almost 3 weeks interval between the first
> and the second scans. I am concerned, therefore, that signal might have
> deteriorated and I'm thus wary of using the intensities data and images
> from the second scan.
>
> My question is therefore, can I convert the original jpeg files in tiff
> format and combine them with locs files from the second scan to import the
> intensities data generated during the first scan using beadarray package.
> My reasoning being that no compression seemingly was applied to jpeg files
> and the same probes should be in different swaths during both first and the
> second scans. Please, correct me if I'm wrong.
>
> Many thanks!
>
> Aliaksei.
>
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-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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