Dear Artur, Any settings for layout that lead to same values for printorder(layout)$printorder will give the same results in normalizeForPrintorder(). Best wishes Gordon On Thu, June 21, 2007 11:17 pm, Artur Veloso wrote: > Dear Gordon, > > thank you very much for your reply. I think my mistake in those regards was > caused by the fact that the function printorder allows one to specify the > number of duplicates in the array. > > In an unrelated issue, I've been using limma to analyze single channel cDNA > arrays and many times ran into errors message like "List must contain > components R and G" generated by the lack of the second channel on my > arrays. My solution was to change the code for almost all the functions that > I used on the pre-processing stage. Basically, I just removed the parts of > the code that referred to the non-existing channel. > I just wanted to bring awareness to this issue and offer to e-mail you the > changes I made on the functions to make them more suitable for my situation. > > All the best, > > Artur Veloso > > On 6/21/07, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: >> >> Dear Artur, >> >> You question doesn't really make sense, because print-order normalization >> has nothing to do with >> duplicated spots. The identities of the probes are ignored in such a >> normalization. In any case, >> you can't move spots around and expect the function to still keep track >> correctly of the print >> order. In the limma package, handling of duplicated spots is done >> post-normalization. >> >> Best wishes >> Gordeon >> >> > Date: Wed, 20 Jun 2007 15:40:18 -0400 >> > From: "Artur Veloso" <abveloso at="" gmail.com=""> >> > Subject: [BioC] how to use normalizeForPrintorder accounting for >> > duplicates when there are spots that are not duplicated in >> the array? >> > To: "Bioconductor List" <bioconductor at="" stat.math.ethz.ch=""> >> > >> > Hi all, >> > >> > I am very new to microarray analysis and I'm running into a few issues >> with >> > normalizations for the print order. The arrays I am working with are >> > "home-made" and the spots are duplicated and separated by columns. >> > >> > My problem arises from the fact that there are non-informative spots ( >> i.e. >> > landing lights and empty spots) that are not duplicated. Would it be >> > acceptable for me to take all these uninformative spots and shift them >> to >> > the end of my spots list so that they didn't interfere with the >> informative >> > and properly duplicated spots? Could this interfere with the results >> that >> > I'd get from the function normalizeForPrintorder? >> > If shifting the position of my spots like that isn't a good idea, does >> > anyone have a suggestion to me? >> > >> > Thank you all very much, >> > >> > Artur Veloso