[BioC] Illumina array quality checking and RegGrn values..

[Johnstone, Alice]

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.