[BioC] converting Affy indices to x,y coordinates

[Kasper Daniel Hansen]

Todd,

This may be a bit hard to explain.  There are essentially two index
numbers: the one used by Bioconductor/aff/affxparser etc. and the one
stored in the CDF file.  The one stored in the CDF file (which you
will never see used in any Bioconductor documentation) is zero-based,
whereas the one "we" use is 1-based.  Why the discrepancy.  Well, I
cannot speak for Affymetrix (but I guess this is caused by C using
zero-based indixes), but in Bioconductor we use 1-based indexing
because if we read an entire CEL file into a vector we want to be able
to do
  vector[INDEX]
and indexing is 1-based in R.

It is pretty clear the documentation in affxparser is a bit unclear
here.  If you are really trying to understand the internals, you will
- aside from reading the affxparser docs - also have to do a fair
amount of experimentation and reading of the affymetrix file format
specs.

Kasper

On Mon, Feb 14, 2011 at 12:52 PM, Todd Allen <genesplicer28 at yahoo.com> wrote:
> Kasper,
>
>   Let me clarify.  I have opened the HGU133 Plus 2 CDF file inside Microsoft notepad, and I can visually see lists of data underneath header information.  I randomly chose  the value of
> 1354890, which I am confident is an authentic affymetrix index for a single, specific affymetrix probe on the chip because of the descriptive header information that is present.
>
> Assuming this value is an authentic index, I was hoping to use the formulas in the affyparser documentation to manually calculate the x & y coordinates of the probe on the affy chip.  As mentioned below, the y coord is coming out correctly, but the x coordinate is off by 1.
>
> So, I am trying to understand if the problem is with something I am doing wrong, or whether the documented formulas in affyparser are somehow off.
>
> Todd
>
>
>
>
> --- On Mon, 2/14/11, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:
>
>> From: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
>> Subject: Re: [BioC] converting Affy indices to x,y coordinates
>> To: "Todd Allen" <genesplicer28 at yahoo.com>
>> Cc: bioconductor at r-project.org
>> Date: Monday, February 14, 2011, 12:12 PM
>> On Mon, Feb 14, 2011 at 11:18 AM,
>> Todd Allen <genesplicer28 at yahoo.com>
>> wrote:
>> > In my own work, I am processing a HGU133Plus 2 CDF
>> file. The array dimensions are (1164, 1164) and if I take
>> the index of a specific probe listed as 1354890, I
>>
>> What exactly do you mean by "I take the index of a specific
>> probe
>> listed as 1354890"?  Listed where, where do you get
>> this number and
>> how do you know what line in the CDF file corresponds to
>> this probe?
>>
>> Kasper
>>
>
>
>
>