Hi, Just a couple of questions about plier a) With justPlier it is possible to specify as an input vector the replicate structure of the batch we want to analyze ('replicate' input option). Can anybody tell me how this information is used by the algorithm? In fact, can anybody point me to some technical references on how plier works? b) I found that the 64-bit compiled version of plier presents some stability issues (i.e. it crashes). A couple of month ago Adai posted a message (http://files.protsuggest.org/biocond/html/9034.html) saying that he solved a similar (I hope) problem. So, Adai, Crispin, anybody, could you please point me in the right direction in order to make plier run under my 64-bit Opteron? Thank you Ariel./ -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339

I had the problem when I was submitting it to a cluster. When I actually ssh-ed into one of the nodes and ran the code interactively, it worked fine. But then I tried with different array type, I had the segment fault even with only 3 arrays. So I am not sure if this is a problem with the cluster queue manager or plier or gcc or something else. Crispin was quite helpful in suggesting to run it interactively, so I hope he finds a solution for you. But I eventually decided not to use PLIER expression measure simply because no documentation was available explaining it. I prefer knowing what I am doing than using a black box systems. I suggest you try RMA or GCRMA which has excellent documentation and has been shown to be better than MAS 5.0 (which is also well documented). Regards, Adai On Thu, 2005-07-21 at 11:37 -0400, Ariel Chernomoretz wrote: <snip> > b) I found that the 64-bit compiled version of plier presents some stability > issues (i.e. it crashes). A couple of month ago Adai posted a message > (http://files.protsuggest.org/biocond/html/9034.html) saying that > he solved a similar (I hope) problem. > So, Adai, Crispin, anybody, could you please point me in the right direction > in order to make plier run under my 64-bit Opteron?