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 > Hi, 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 more. 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: ----------- Axis-invertX=0 AxisInvertY=0 swapXY=0 ----------- 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 week-end. Hopin' it helps, Laurent -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent