Sweet.
Works fantastically.
Thankyou everyone for your assistance!

Regards
Omri Yahel
MSc Student
School of Biological Sciences
University of Auckland, New Zealand

On Mon, Dec 15, 2008 at 4:48 PM, Kasper Daniel Hansen <
khansen@stat.berkeley.edu> wrote:

> There is a 1-1 correspondance between the indices in the matrix and the
> (x,y) position of the probe on the chip. See the functions xy2i and i2xy for
> details. Converting from (x,y) to indices gives you a unique identifier
> instead of 2-dimensional identifier. It has the side product of being very
> useful for indexing.
>
> So the only way you can get from your list of probes to the numbers in the
> matrix is if you have (x,y) positions for the probes.
>
> Kasper
>
>
> On Dec 14, 2008, at 17:22 , Omri Yahel wrote:
>
>  Thankyou for your help
>> That clears a few things up, however I'm still having some problems...
>>
>> I can use;
>>
>>  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
>>
>> to form the AffyIDs I want, but I'm having trouble understanding what the
>> pm
>> and mm colums in that matrix are.
>>
>> I have a list of probes which I would like to label with probe ID's. Since
>> I
>> know the ProbeSetID for each probe I can look at the matrix of the probe
>> set
>> as above. My probe will be one of those 11.
>>
>> How do I work out which of the 11 probes in above matrix is my probe? Can
>> those values be related to the Probe Interrogation position? What exactly
>> are those values?
>>
>> Thanks again for any help
>> Omri
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Dec 15, 2008 at 10:06 AM, James MacDonald <jmacdon@med.umich.edu
>> >wrote:
>>
>>  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@gmail.com> 12/14/08 3:26 PM >>>
>>>>>>
>>>>> On Sat, Dec 13, 2008 at 1:46 AM, Sean Davis <seandavi@gmail.com>
>>> wrote:
>>>
>>>  On Fri, Dec 12, 2008 at 4:01 AM, Omri Yahel <omri.yahel@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
>>>
>>>       [[alternative HTML version deleted]]
>>>
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