[BioC] marrayInfo linked to marrayRaw

[michael watson (IAH-C)]

Hi

Apologies if this is a stupid question, but I am just trying to figure out the internal workings of the marray* classes.

OK, lets say I have a genepix results file, so in that file I have Block, Column, Row, ID, Name and Expression values. 

Now lets say I also have an annotation file that has spot annotations in it.  This also has Block, Column, Row and then gene annotation columns.

Now as I understand it, what I should do is:

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?

Thanks
Mick