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.

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