The "no-brainer" solution is to presort the arrays by mer-label. That would make the spacing=1. --Naomi At 02:07 PM 10/8/2008, Christine Voellenkle wrote: >Dear all, > >I perform 2 color hybridization, using microRNA and Exiqon slides. >slide design: 4 replicates of 1 array > each array consits of 8 subarrays, > each subarray of 16 columns and 11 rows > each mir has 4 replicates > >For analysis of the data I use limma GUI, to obtain the p-values of >differentially expressed mirs I carried out loess normalization >(backgroundsubstraction normexp, offset=10) and subsequently applied the >Linear model fit, which works, as long as I treat each replicate like a >single mir. >I would like to now also about the correlation of the replicates, so I >entered as replicate number 4 and as distance 21 (according to >"Bioinformatics+ computional statistics using R and Bioconductor" the >distance corresponds to the number of spots that lies betweeen the >replicates). >But I get the following message: > >"Error in dim(M)<- c(spacing,ndups, ngroups, nslides) >dims[product 5628] do not match the length of object [5632]" > >I rechecked the gal file and recounted on the image, 21 is the correct >number (considering the column-distance, using the number of spots of row >distance results in dims[product 0]). >I read the limma guide and checked also the examples on the limma gui >homepage, but it's always either no replicate or only 2 replicates next to >each other. >Do you know a solution? > >Also another question: >IF one day I manage to do the duplicate correlation and given that I would >use weights to identfy features with the flag "bad", how will the software >handle this if one or more replicates are flagged bad? will it exclude the >flagged bad replicate from the correlation? >If yes, is there a way to put a minimum limit of 2 unflagged spots per mir, >so that in case of only 1 unflagged replicate of a mir to exclude this mir >from analysis? > >Thank you a lot in advance! >Greetings, Christine > > > > > > > > >Dr. Christine V?llenkle, Ph.D. >Research Laboratories-Molecular Cardiology >I.R.C.C.S. Policlinico San Donato >Via R. Morandi, 30 >20097 S. Donato M.se (MI) Italy >Phone: +39 02 52774 683 (lab) > +39 02 52774 533 (office) >Fax: +39 02 52774 666 >email: christine.voellenkle at gmail.com > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111