[BioC] PM or MM spot intensities from CEL files

James MacDonald jmacdon at med.umich.edu
Thu Nov 25 13:58:32 CET 2004

Your question is not very clear, but I will assume that what you want to
extract are the pixel intensities for each probe (each probe is in only
one spot, so AFAIK, these terms are interchangeable), rather than the
75th percentile of these values (the cel file contains the 75th
percentile, not the mean value). The short answer is no. The cel file
only contains these 75th percentile values. If you want all the pixel
intensities for each spot, you need the dat file. 

Unfortunately, there is no functionality that I know of for extracting
these pixel intensities in BioC. The dat file is simply a 16-bit tiff
file, so you need some method to place a grid on the image and then
extract each pixel intensity value for each spot.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Tapan Mehta <tapmehta at yahoo.com> 11/25/04 12:55 AM >>>

I would really appreciate if somebody could tell
whether it is possible to extract PM and MM spot (not
probe) intensities from CEL files. A CEL file has X
and Y coordinates and mean intensity associated with
each of these locations. I think each spot in an
Affymetrix array is either a perfect match or
mismatch. Although there is a method in the affy
package to extract PM and MM values for each probe I
found no method to find PM or MM spot intensity from
CEL files.

Thanking you in advance,

Tapan Mehta

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