[BioC] Expired Illumina expression chip - advice for use and experimental design

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Thu Jan 31 21:54:07 CET 2008

This is an experimental design question, not a trouble with bioconductor
question (yet!!) so apologies for being slightly off-topic. But I am
hoping to tap this wealth of knowledge for some advice beforehand to
save me problems during later analysis.

We have two (separate) expression experiments to run on the Illumina
ratref12 chips over a total of three chips.  However one of the chips
(ordered for a previous experiment and not used) is now two months past
its expiry date.  My first question is does anyone have any experience
with using data from an expired chip compared with a new chip and will
it give results that are different enough to cause worry?  
It still costs whether we use it or not, and unfortunately (as always)
money and samples are of limited supply.

The second question is:
If we do go ahead, in terms of analysis design, what is the best way to
distribute samples to account for this difference over the two new, one
old chip (each with 12 slots).

The two experiments to be analysed are as follows:
3 groups of n=5
Group 1 drug A
Group 2 drug B
Group 3 saline control
Total n=15
Aim: to compare the effect of each drug on expression, and potentially
identify similarities, ie from A-saline, B-saline.

7 sets of dose linked-triads
Each triad has three rats:
1 drug C+D
1 drug C 
1 drug D
Total n=21
Aim: to identify differences in expression from the drug combinatorial
effect, ie (drug C+D)-(drug C)-(drug D) (I think?).

Third and final question:
I was thinking of using a block effect with limma to combat the spread
of data over different chips, and potentially using weighting as well
(if the chips do prove to be different) or will I hit difficulties with
the within chip vs between chip variation? 
Any advice you can offer on better ways to approach this would be much

Thank you for your time,

Alice Johnstone

PhD Student
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
New Zealand

Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770

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