Question: Probe IDs VS Probeset IDs in Yeast2 annotation
0
gravatar for Omri Yahel
10.8 years ago by
Omri Yahel70
Omri Yahel70 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. Any help very appreciated! Omri Yahel MSc Student School of Biological Sciences University of Auckland, New Zealand [[alternative HTML version deleted]]
yeast2 probe • 509 views
ADD COMMENTlink modified 10.8 years ago by James W. MacDonald51k • written 10.8 years ago by Omri Yahel70
Answer: Probe IDs VS Probeset IDs in Yeast2 annotation
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gravatar for Sean Davis
10.8 years ago by
Sean Davis21k
United States
Sean Davis21k 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
ADD COMMENTlink written 10.8 years ago by Sean Davis21k
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]]
ADD REPLYlink written 10.8 years ago by Omri Yahel70
Answer: Probe IDs VS Probeset IDs in Yeast2 annotation
0
gravatar for James W. MacDonald
10.8 years ago by
United States
James W. MacDonald51k 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at 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
ADD COMMENTlink written 10.8 years ago by James W. MacDonald51k
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]] > > _______________________________________________ > 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]]
ADD REPLYlink written 10.8 years ago by Omri Yahel70
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=YEAS T_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 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.8 years ago by Kasper Daniel Hansen6.4k
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]]
ADD REPLYlink written 10.8 years ago by Omri Yahel70
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