[BioC] how to get mismatch probe coordinates

[James W. MacDonald]

ulas karaoz wrote:
> thanks. That is not exactly what i meant, what i meant was given a 
> probe's coordinates from the AFFY files, i.e. HG-U133A_probe_tab, how do 
> I figure out the coordinates for the corresponding mismatch probe.
> Is this info stored somewhere if i read the cdf file with read.cdffile 
> in makecdfenv package?
> thanks.

Although indexProbes only gets you the index for a given probe, this 
information can be used to get the xy coordinates and show you how 
things are arranged on the chip.

 > dat <- ReadAffy()
 > indexProbes(dat, "pm")["1007_s_at"]
$"1007_s_at"
  [1] 129340 213420 396671  82246 430968 427082 432610  72465 432865 
99501 504952 443862 341432 198778
[15] 463575  10989

 > indexProbes(dat, "mm")["1007_s_at"]
$"1007_s_at"
  [1] 130052 214132 397383  82958 431680 427794 433322  73177 433577 
100213 505664 444574 342144 199490
[15] 464287  11701

 > i2xy(129340)
        x   y
[1,] 467 181
 > i2xy(130052)
        x   y
[1,] 467 182

So the mm probes are located directly under the pm probes. Therefore, 
the coordinates of the mm probe are x and y+1, where (x,y) are the pm 
coordinates.

Jim



-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109