Dear all, I am trying to analyze some agilent chip for the first time, therefore terrible confused. I would really appreciate any kind of suggestion or help. The source of the data is http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5914 and the platforms are Mouse Development (44K) Microarray V 2.1 and v2.2. After importing the data in to bioconductor environment using "read.maimages" function I have been trying to use normalizeWithinArrays and then normalizeBetweenArrays. normalizeWithinArrays function requires layout (list specifying the dimensions of the spot matrix and the grid matrix). I am having trouble creating this layout object. I am trying "read.marrayLayout" function to accomplish this task and have no clue how to compile the argument values (i.e. fname, ngr, ngc, nsr, nsc etc). I am also not sure how to find the file that stores plate and control information for my particular chip. Thanks in advance. [[alternative HTML version deleted]]

Daer Nayeem, If you are trying to use "normalizeWithinArrays" function, its a function from the limma package and you don't need read.marryLayout for it. Use read.maimages specifying the appropriate platform. If you have a GAL file containing the gene list info, you can then use "getLayout" or "readGAL" in limma to read in print-layout info. Cheers Jean On Wed, 17 Sep 2008, Nayeem Quayum wrote: > Dear all, > > I am trying to analyze some agilent chip for the first time, > therefore terrible confused. I would really appreciate any kind of > suggestion or help. The source of the data is > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5914 and the platforms > are Mouse Development (44K) Microarray V 2.1 and v2.2. > > After importing the data in to bioconductor environment using > "read.maimages" function I have been trying to use normalizeWithinArrays and > then normalizeBetweenArrays. normalizeWithinArrays function requires layout > (list specifying the dimensions of the spot matrix and the grid matrix). I > am having trouble creating this layout object. I am trying > "read.marrayLayout" function to accomplish this task and have no clue how to > compile the argument values (i.e. fname, ngr, ngc, nsr, nsc etc). I am also > not sure how to find the file that stores plate and control information for > my particular chip. Thanks in advance. > > [[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 >