Hi John, This is my first to handle the Agilent 4x44k arrays. Yes you are right. My collaborator ran 9 chips and sent me 36 separate files. For "read.maimages" they should serve as individual data files to read in just like regular arrays. Am I right? Is there any other file(s) which need to be read in? best, JP- --On Monday, October 29, 2007 5:26 PM -0700 John Fernandes <jfernand at="" stanford.edu=""> wrote: > The Feature Extraction software from Agilent knows the format from the > control file supplied by Agilent and will create 4 sets of separate > files. You run your analysis as if they were singly hybridized 44K > arrays. > > John > > >> Thanks Yong! >> >> Your way may be a good one for "normalizeWithArrays" to work in a regular >> manner. But it may be questionable if you need to apply >> "normalizeBetweenArrays". My data set used common reference design. I may >> want to carry out normalization between arrays. >> >> I read in data using "read.maimages" with source="agilent". There should >> be some standard ways by which I can run normalization within arrays. Am >> I correct? >> >> best, >> >> JJ- >> >> --On Monday, October 29, 2007 2:51 PM -0500 Yong Yin >> <yyin at="" watson.wustl.edu=""> wrote: >> >>> If you are asking how to handle different blocks in Agilent 4x44k, we >>> have had the same problem. >>> >>> >>> In brief, we have printed the same set of 44k probes on each of the 4 >>> blocks, and we are applying different samples onto different blocks. >>> >>> >>> After discussing with our microarray facility, they find a way to >>> generate individual raw data file for each array using the software >>> coming with scanner. Then I just treat data generated from different >>> blocks as independent arrays. >>> >>> >>> I suggest you talk to the people running the machines. And I would love >>> to hear others' experiences. >>> >>> >>> Best, >>> >>> >>> Yong >>> >>> >>> ? >>> >>> >>> On Oct 29, 2007, at 2:19 PM, Jianping Jin wrote: >>> >>> >>> Dear list, >>> >>> >>> When I was trying the normalizeWithinArrays function of limma I got an? >>> error: Error in switch (method, loess = {: Layout argument not >>> specified).? >>> I was using an Agilent 4 x 44k data set and knew the Agilent printer >>> has? only one block (Row and Col having been taken already). How can I >>> do loess? >>> normalization for each slide? Should I add a Block column into the RG, >>> the? >>> data read-in file in order to do normalizaWithinArrays? >>> >>> >>> Another question is that is there any easy way I can remove all >>> control? spots from all data files? >>> >>> >>> Appreciate your help! >>> >>> >>> JJ >>> >>> >>> ################################## >>> Jianping Jin Ph.D. >>> Bioinformatics scientist >>> Center for Bioinformatics >>> Room 3133 Bioinformatics building >>> CB# 7104 >>> University of Chapel Hill >>> Chapel Hill, NC 27599 >>> Phone: (919)843-6105 >>> FAX: ? (919)843-3103 >>> E-Mail: jjin at email.unc.edu >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> >>> >>> Yong Yin, Ph.D. >>> >>> >>> Senior Scientist >>> Genome Sequencing Center >>> Washington University School of Medicine,?Campus box 8501 >>> 4444 Forest Park >>> Saint Louis, MO 63108 >>> >>> >>> Tel: (314) 286-1415 >>> >> >> >> >> ################################## >> Jianping Jin Ph.D. >> Bioinformatics scientist >> Center for Bioinformatics >> Room 3133 Bioinformatics building >> CB# 7104 >> University of Chapel Hill >> Chapel Hill, NC 27599 >> Phone: (919)843-6105 >> FAX: (919)843-3103 >> E-Mail: jjin at email.unc.edu >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104, Campus Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at unc.edu