[BioC] Re: a bug? non agreement btw. indexProbes and affy CDF file

[ulas karaoz]

thanks for all the help, i have tried to do some comparison with the 
values you have provided:
In the AFFY CDF file for U133A chip, the following line is for the 
x=467, y=181:
Cell1=467       181     N       control 1007_s_at       0       13      
G       C       G       0       129339  -1      -1      99
and to x=467, y=182:
Cell2=467       182     N       control 1007_s_at       0       13      
G       G       G       0       130051  -1      -1      99


Why these indices are offset by 1 compared to yours, has this anything 
to do with the package wide xy.offset = 1 option?
I am very puzzled about what are the correct indices, can I plug in 
simply the indices from the CDF file, which seem to be computed as: x+ 
(712 * y) for U133A chip. Clearly I am missing something.
thanks.




On Nov 1, 2004, at 9:21 AM, James W. MacDonald wrote:

> 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
>
--------------------------------------------
Ulas Karaoz
Boston University
Ph.D.Student in Bioinformatics
zlab.bu.edu