Dear Aliaksei,

If I was checking this I'd start by simply reading the two text files using
read.table() and comparing the two vectors of intensities.  I presume
you're worried that the sample will have degraded over time or a second
scan will have photo-bleached the sample, so you want to check that the
distribution of intensities hasn't changed to much.  Using density() on the
intensities and then plotting the output from that should suffice, although
you'll probably want to do that on the log scale.  If the sample has
significantly degraded then you'll see a much narrower and taller peak  at
the low end.

Most of the Illumina arrays also have negative control probes, so you can
use the annotation to identify these and then see how many probes rank
higher than them.  If they move significantly then you know there's
something different between the two scans.  You'll have to use your
own judgement on "significantly" as there will always be some fluctuation.

Mike

On Tue, Dec 20, 2011 at 9:09 PM, Salvador <salvador@bio.bsu.by> wrote:

> Dear Mike,
>
> Thanks for the quick response. It explained a lot. I'm still awaiting the
> data from the second scan. Hopefully the intensities won't be too
> different. I don't want to seem cheeky, but am very new to R and microarray
> analysis in particular. So any suggestions on how to use R to run a
> comparison between the scans would be greatly appreciated. All I can think
> of is building an MA plot for each sample's intensities from first and
> second scans. But even then, what would I consider to be "very different".
> I.e. is there any quantitative parameter I could use to decide, whether the
> data from the two arrays if comparable.
>
> Many thanks,
>
> Aliaksei.
>
> На 19.12.2011 18:41, Mike Smith напісаў(ла):
>
>> 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
>> <mailto: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
>>
>>
>


-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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