[BioC] Probe IDs VS Probeset IDs in Yeast2 annotation

[Kasper Daniel Hansen]

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 at 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 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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>>
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