[BioC] marrayInfo linked to marrayRaw

Jean Yee Hwa Yang jean at biostat.ucsf.edu
Thu Aug 28 13:08:21 MEST 2003

1) create a layout object using read.marrayLayout 
2) read in the annotations file using read.marrayInfo 
3) read in the gpr file using read.GenePix setting the layout parameter to
the layout object I created and the gnames parameter to the marrayInfo object I created.

> Now, what I want to know is this - DOES read.GenePix associate spot
> annotations to expression values using Block, Column and Row, or does
> it associate them based on the order of rows in the file?  Put another
> way, if my spot annotation file is ordered alphabetically on, say,
> gene name, and my gpr file is ordered on (Block, Column, Row), will I
> associate the wrong gene names with the wrong spots?  Put a third way,
> does my annotation file that I read into marrayInfo object have to
> have the spots in the SAME ORDER as the genepix results file?
Yes.  I usually create the layout information using the same gpr
files.  YOu can read a gpr file in with the function read.Galfile and that
will return a list of two components
1) Layout parameter
2) Gene Names annotation.



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