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Hi Dipen, If I am understanding you correctly, you have two different sets of gpr files. Both sets have the same gene/spot IDs, but they were printed in a different order, correct? I'm not exactly sure how read.maimages reads in the $genes information (i.e., block, row, column, id, etc.), but it might just read it from the first gpr file. If so, the intensities for all the gpr files of this type should be correct, but the other .gpr files will be incorrect. If not, what do you mean when you say that it is "collating the gene-intensity information" ? You could manually go into the gpr files of one type and sort the spot IDs so they are in the same order as the other gpr type, but I wouldn't recommend this approach. Because the two gpr files have different spatial arrangements of the genes, any normalization that takes into account spatial location (e.g., print-tip loess within-array normalization) would be done incorrectly for the re-ordered gpr files. The second, better approach would be to read in each set of gpr files separately, do any spatially-dependent normalization separately (which are done per array, so doing them in separate groups won't matter), then sort them so they both have the same spot order and merge them together using merge(). You might have to replace the block, row, column info of one set with the other set for merge() to work properly, but as long as it's AFTER doing any spatially-based corrections, it will be fine. This second approach will also work well if there are differences in the total number of spots or numbers of blanks, buffers, etc. You'll have to remove all the blank and buffer spots from each set before merging. HTH, Jenny At 09:43 AM 1/11/2007, Dipen Sangurdekar wrote: >Hello > >When I attempt to read in different gpr files (originating from slightly >different print files, but with same gene IDs) for the same experimental >setup, limma makes errors in compiling the RG file. The wrong intensity >values are associated with a particular gene across the arrays. > >Is there a quick way to get around the problem, that avoids collating >gene-intensity information from each gpr? > >Thanks >Dipen > > [[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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu