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: Exp1 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. Exp2 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 appreciated! 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 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.