Hi Scott, I replied on this topic earlier today. >From what we've seen looking at the Agilent chips from our labs (mice and human, 1x44 and 4x44 chips, made by several people), duplicate probes on a chip give more or less identical results. I'll let others say if it's appropriate to use blocking variable that way, but I do not think the result would be very meaningful. It would give you an estimate of a intra-chip technical variation that is basically negligible compared to inter-chip technical variation. Dealing with those duplicate probes "properly" would be a lot of work, and I think it would give you very little at the end. We look at them as a control that the signal from a given probe is reproducible and then ignore them afterward. Francois On Mon, 2007-07-16 at 16:23 -0500, Franklin, Scott wrote: > I am very new to microarray experiments and have a question with > calculating > duplicate correlations for 4x44 Agilent chips. > > After searching extensively through the bioconductor mailing list > submissions, I have seen that no one has come up with a solution to > handling > a variable number of gene replicates on the same chip. As I understand > it, > limma was not designed to handle this. > > Before seeing that this was not a functionality of limma, we attempted > to > treat each individual gene as a block. We sorted by probe name, then > assigned a unique number to each probe name with it repeating the number > of > times that gene appears on the chip. We ended up with roughly 21,000 > blocks. I had assumed that duplicate correlation would compute a > correlation for each of these blocks. > > Is this a reasonable approach or a complete misunderstanding of the > blocking > variable? (By the way, the calculation is still running after an hour) >