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
See the information from Affy:
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)
[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))
You can also get comparable information from the yeast2probe package
James W. MacDonald, M.S.
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
>>> "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="">
> 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
> > Currently I can only find probeset IDs. That is, one AffyID for
> > 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.
I've looked in the yeast2cdf package, all I see is functions
which convert x-y coordinates on the chip (1-496) to a single number
(from 1 to 246016).
I am looking for affyIDs for each probe in the form 1780100_at1
There should be 11 (or maybe 22) such affyIDs per probe set.
Any further help would be greatly appreciated.
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