Hi Alice:

    I do not think you should worry too much about the registration 
values of your arrays. We have several Illumina arrays which had 
registration values close to 0. However I did not see any problems with 
these arrays. Below is the answer from Illumina technical support when I 
asked them the similar question:

The 0 in the metrics file may indicate that there is a problem with 
registration of the stripe but there are other ways to look at this.  
First, have you looked at the data from the Beadchip in BeadStudio?  
Does the data appear consistent with the rest of the samples in your 
experiment?  In addition, do the controls look OK for this sample when 
compared to the other samples?    

Next, you can look at the registration visually in BeadStudio as long as 
you have saved tif images when you scanned the BeadChip.  To do so, go 
to the Analysis menu in BeadStudio and select View Image then choose the 
stripe you are interested in.  Now select Overlay Cores (the icon looks 
like 3 blue-green circles) and look at the image to see if the green 
circles line up with the intensity spots on the image.  If the BeadChip 
is not registered the circles representing cores will not line up with 
the spots on the array and the circles themselves will be somewhat 
disordered.  

If you have reason to suspect that registration is affecting your data, 
you can rescan the BeadChip.  Gene expression BeadChips can be rescanned 
as long as you do so within a few days and if the BeadChips have been 
stored in the dark. If you do recan the BeadChip, please uncheck  "Save 
Compressed Images"; this will allow you to save tif images.


Cheers,
------------------------------
Wei Shi, Ph.D
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville 3050, VIC
Australia

Johnstone, Alice wrote:
> Hi there, 
>
> My first question is what methods/packages are available for quality
> checking of Illumina expression arrays?
>
> This is because I have just received data back from an Illumina Rat
> tissue expression experiment and while looking for info on beadlevel
> analysis I came across this post:
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/1572
> 0/focus=15744
>
> In which Matt Richie states that the RegGrn values should be
> approximately 1..  for the array data I have back only 2 arrays per chip
> have RegGrn values of 1 the rest sit at ~0.08! Can anyone provide me
> with some more information on what the metrics should look like?
>
> I was expecting one of my 3 chips to be of poorer quality but not
> all....  
>
>
> Thank you very much!
>
> Alice Johnstone
>
> PhD Student
> Institute of Environmental Science and Research Ltd
> Kenepuru Science Centre
> 34 Kenepuru Drive
> PO Box 50-348
> Porirua
> New Zealand
>
> Tel:  + 64 4 914-0717
> Fax: + 64 4 914-0770
>
>
> P Think before you print
> This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed.
> If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>   

	[[alternative HTML version deleted]]

