[BioC] Probe IDs VS Probeset IDs in Yeast2 annotation

[James MacDonald]

Hi Omri,

There aren't individual IDs for the probes in a probeset. The fact that e.g., 1780100_at gets the 1:11 appended to the end is because in certain situations (such as a data.frame) the rownames have to be unique, so R will mangle the name by adding a number in order to make them unique.

See the information from Affy:

https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=YEAST_2%3A1780100_AT

You can arbitrarily create the names appended with numbers, as long as you know how many probes per probeset. This information is contained in the yeast2cdf package as Sean noted.

> get("1780100_at", yeast2cdf)
          pm     mm
 [1,] 242032 242528
 [2,] 240060 240556
 [3,]  44405  44901
 [4,]   5840   6336
 [5,]  63999  64495
 [6,] 155680 156176
 [7,]   2645   3141
 [8,] 180366 180862
 [9,]  81113  81609
[10,] 234852 235348
[11,] 148373 148869

or more directly,

> dim(get("1780100_at", yeast2cdf))[1]
[1] 11

You can also get comparable information from the yeast2probe package as well.

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
>>> "Omri Yahel" <omri.yahel at gmail.com> 12/14/08 3:26 PM >>>
On Sat, Dec 13, 2008 at 1:46 AM, Sean Davis <seandavi at gmail.com> wrote:

> On Fri, Dec 12, 2008 at 4:01 AM, Omri Yahel <omri.yahel at gmail.com> wrote:
> > Hello
> >
> > I am trying to extract affyIDs for individual Probes on the yeast2
> platform.
> >
> > Currently I can only find probeset IDs. That is, one AffyID for each 11
> > mismatch-perfectmatch pairs.
> > The yeast2.db and yeast2probe package's don't seem to help me.
> >
> > Where can I get probe level identifiers for this platform.
>
> Hi, Omri.
>
> You'll want to look at the yeast2cdf package.
>
> Sean


Hi, Sean

I've looked in the yeast2cdf package, all I see is functions
i2xy(i)      and
xy2i(x,y)
which convert x-y coordinates on the chip (1-496) to a single number index
(from 1 to 246016).

I am looking for affyIDs for each probe in the form  1780100_at1
1780100_at2 etc.
There should be 11 (or maybe 22) such affyIDs per probe set.

Any further help would be greatly appreciated.
Regards
Omri

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