[BioC] marrayInfo linked to marrayRaw

Naomi Altman naomi at stat.psu.edu
Thu Oct 2 11:07:29 MEST 2003

I am not sure I totally understand how things work.

We were recently given some .gpr files that were 32 blocks each 23x24.

The GAL file stated that the array was 32 x 22 x 24, and gave gene names 

Sure enough, the last row in each block is empty, and is flagged as such.

1. So ... do we need to create a set of gene names for these empty rows or 
not?  We tried changing the GAL file by changing 22 to 23 and adding some 
NA's for the missing names, and we did not get the same list of gene names.

2. How can we access the raw or normalized data by gene-name?

Naomi Altman

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.

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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