[BioC] How to create marrayLayout for Agilent Mouse Development 44K microarray

[Jean Yee Hwa Yang]

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.
>
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>
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