[BioC] Re: AFFY package for R, image of cell file turned upside down?

Laurent Gautier laurent@cbs.dtu.dk
Wed, 2 Oct 2002 22:05:02 +0200

On Wed, Oct 02, 2002 at 02:09:00PM +0200, Jesper Ryge wrote:
> Hi laurent
> I am using the affy package for R.  I just have one question.  I tried to 
> read a cell file and plot it with image(cel.file).  That works fine, except 
> the image is turned upside down!  It is a rat neuro chip, so  there is a 
> control sequence in the top of the chip that reads "genechip Rat neurochip" 
> if the spike-ins hybridize OK.   But this is now shown in the bottom of the 
> image an upside down?  How is that?
> Jesper Ryge


I CC'ed this to bioconductor as it might be of interest to others.

The chip image seems flipped with the Hu6800 too
(my benchmark since it is the first Affymetrix cheap I met)

When a CEL files is parsed, the intensity values are stored in a
matrix (using the X and Y to index the row and column respectively).
You may want to read the affy.pdf vignette around the page 18 to know

However, there is something I realized quite recently (and I am
about to address for the next version of the package).
There is something like follows in the header of
CEL files:

I never found files where it was set to one, so the code is not
looking closely at the values of these properties. I would appreciate
reports about CEL where the values change.

In the meanwhile I'll add a little something to make the parser yell
if the values change (just in case). 'should be in BioC by this

Hopin' it helps,


Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent