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=YEA ST_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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]