probe level annotation
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 8.8 years ago
Hi list, I found the XY coordinates for the probes in 'hgu133aprobe' are not exactly the same as those shown on NetAffx.com. Please see below. Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for examples, the same as in 'hgu133aprobe'? thanks, ...Tao > R.Version() $platform [1] "i386-pc-mingw32" $arch [1] "i386" $os [1] "mingw32" $system [1] "i386, mingw32" $status [1] "" $major [1] "2" $minor [1] "3.0" $year [1] "2006" $month [1] "04" $day [1] "24" $`svn rev` [1] "37909" $language [1] "R" $version.string [1] "Version 2.3.0 (2006-04-24)" > library(hgu133aprobe) > data(hgu133aprobe) > as.data.frame(hgu133aprobe[1:16,]) sequence x y Probe.Set.Name Probe.Interrogation.Position Target.Strandedness 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at 3330 Antisense 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at 3443 Antisense 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at 3512 Antisense 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at 3563 Antisense 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at 3570 Antisense 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at 3576 Antisense 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at 3583 Antisense 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at 3589 Antisense 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at 3615 Antisense 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at 3713 Antisense 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at 3786 Antisense 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at 3793 Antisense 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at 3799 Antisense 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at 3807 Antisense 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at 3871 Antisense 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at 3878 Antisense > package.version('hgu133aprobe') [1] "1.12.0" And from NetAffx.com Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation Position Target Strandedness CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 8.8 years ago
Hi Jim, Thanks! My bad. I accidentally selected the HT 133A array. Any idea on my second question? I assume they are listed in the same order, but not sure whether it's right. ...Tao ----- Original Message ---- From: James W. MacDonald <jmacdon@med.umich.edu> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Monday, October 2, 2006 1:36:35 PM Subject: Re: [BioC] probe level annotation Hi Tao, I just checked netaffx, and I get the same as the hgu133aprobe and hgu133acdf show: CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense No idea why you got something different. Best, Jim Shi, Tao wrote: > Hi list, > > I found the XY coordinates for the probes in 'hgu133aprobe' are not exactly the same as those shown on NetAffx.com. Please see below. > > Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for examples, the same as in 'hgu133aprobe'? > > thanks, > > ...Tao > > > >>R.Version() > > $platform > [1] "i386-pc-mingw32" > > $arch > [1] "i386" > > $os > [1] "mingw32" > > $system > [1] "i386, mingw32" > > $status > [1] "" > > $major > [1] "2" > > $minor > [1] "3.0" > > $year > [1] "2006" > > $month > [1] "04" > > $day > [1] "24" > > $`svn rev` > [1] "37909" > > $language > [1] "R" > > $version.string > [1] "Version 2.3.0 (2006-04-24)" > > >>library(hgu133aprobe) >>data(hgu133aprobe) >>as.data.frame(hgu133aprobe[1:16,]) > > sequence x y Probe.Set.Name Probe.Interrogation.Position Target.Strandedness > 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at 3330 Antisense > 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at 3443 Antisense > 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at 3512 Antisense > 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at 3563 Antisense > 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at 3570 Antisense > 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at 3576 Antisense > 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at 3583 Antisense > 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at 3589 Antisense > 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at 3615 Antisense > 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at 3713 Antisense > 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at 3786 Antisense > 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at 3793 Antisense > 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at 3799 Antisense > 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at 3807 Antisense > 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at 3871 Antisense > 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at 3878 Antisense > >>package.version('hgu133aprobe') > > [1] "1.12.0" > > > And from NetAffx.com > > Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation > Position Target Strandedness > CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense > GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense > TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense > AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense > TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense > TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense > TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense > ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense > TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense > AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense > TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense > TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense > GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense > GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense > TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense > ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Hi Tao, at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and pm(...) slightly differ. Best, Holger -------- Original-Nachricht -------- Datum: Mon, 2 Oct 2006 13:53:00 -0700 (PDT) Von: "Shi, Tao" <shidaxia at="" yahoo.com=""> An: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> Betreff: Re: [BioC] probe level annotation > Hi Jim, > > Thanks! My bad. I accidentally selected the HT 133A array. > > Any idea on my second question? I assume they are listed in the same > order, but not sure whether it's right. > > ...Tao > > > > > ----- Original Message ---- > From: James W. MacDonald <jmacdon at="" med.umich.edu=""> > To: "Shi, Tao" <shidaxia at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Monday, October 2, 2006 1:36:35 PM > Subject: Re: [BioC] probe level annotation > > Hi Tao, > > > > I just checked netaffx, and I get the same as the hgu133aprobe and > > hgu133acdf show: > > > > CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense > > GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense > > TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense > > AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense > > TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense > > TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense > > TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense > > ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense > > TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense > > AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense > > TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense > > TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense > > GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense > > GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense > > TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense > > ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense > > > > No idea why you got something different. > > > > Best, > > > > Jim > > > > > > > > > > > > Shi, Tao wrote: > > > Hi list, > > > > > > I found the XY coordinates for the probes in 'hgu133aprobe' are not > exactly the same as those shown on NetAffx.com. Please see below. > > > > > > Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for > examples, the same as in 'hgu133aprobe'? > > > > > > thanks, > > > > > > ...Tao > > > > > > > > > > > >>R.Version() > > > > > > $platform > > > [1] "i386-pc-mingw32" > > > > > > $arch > > > [1] "i386" > > > > > > $os > > > [1] "mingw32" > > > > > > $system > > > [1] "i386, mingw32" > > > > > > $status > > > [1] "" > > > > > > $major > > > [1] "2" > > > > > > $minor > > > [1] "3.0" > > > > > > $year > > > [1] "2006" > > > > > > $month > > > [1] "04" > > > > > > $day > > > [1] "24" > > > > > > $`svn rev` > > > [1] "37909" > > > > > > $language > > > [1] "R" > > > > > > $version.string > > > [1] "Version 2.3.0 (2006-04-24)" > > > > > > > > >>library(hgu133aprobe) > > >>data(hgu133aprobe) > > >>as.data.frame(hgu133aprobe[1:16,]) > > > > > > sequence x y Probe.Set.Name > Probe.Interrogation.Position Target.Strandedness > > > 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at > 3330 Antisense > > > 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at > 3443 Antisense > > > 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at > 3512 Antisense > > > 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at > 3563 Antisense > > > 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at > 3570 Antisense > > > 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at > 3576 Antisense > > > 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at > 3583 Antisense > > > 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at > 3589 Antisense > > > 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at > 3615 Antisense > > > 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at > 3713 Antisense > > > 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at > 3786 Antisense > > > 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at > 3793 Antisense > > > 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at > 3799 Antisense > > > 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at > 3807 Antisense > > > 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at > 3871 Antisense > > > 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at > 3878 Antisense > > > > > >>package.version('hgu133aprobe') > > > > > > [1] "1.12.0" > > > > > > > > > And from NetAffx.com > > > > > > Probe Sequence(5'-3') Probe X Probe Y Probe > Interrogation > > > Position Target Strandedness > > > CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense > > > GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense > > > TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense > > > AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense > > > TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense > > > TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense > > > TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense > > > ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense > > > TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense > > > AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense > > > TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense > > > TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense > > > GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense > > > GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense > > > TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense > > > ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense > > > > > > _______________________________________________ > > > 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 > > > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > 734-647-5623 > > > > > > ********************************************************** > > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues. > > _______________________________________________ > 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 --
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Holger Schwender wrote: > Hi Tao, > > at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and pm(...) slightly differ. It depends on what we get from Affy. The probe packages are based on the Affymetrix XXX_probe_tab files, which list things out a particular order, and the cdfs are based on the cdf files. If Affy happened to list things out in the same order for both input files, then things will line up. If not, then they won't ;-D As Holger says, these two are slightly different. I wouldn't be surprised if that were true for all the chips (and I wouldn't be surprised if some were 100% consistent either...). Best, Jim > > Best, > Holger > > > -------- Original-Nachricht -------- > Datum: Mon, 2 Oct 2006 13:53:00 -0700 (PDT) > Von: "Shi, Tao" <shidaxia at="" yahoo.com=""> > An: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > Betreff: Re: [BioC] probe level annotation > > >>Hi Jim, >> >>Thanks! My bad. I accidentally selected the HT 133A array. >> >>Any idea on my second question? I assume they are listed in the same >>order, but not sure whether it's right. >> >>...Tao >> >> >> >> >>----- Original Message ---- >>From: James W. MacDonald <jmacdon at="" med.umich.edu=""> >>To: "Shi, Tao" <shidaxia at="" yahoo.com=""> >>Cc: bioconductor at stat.math.ethz.ch >>Sent: Monday, October 2, 2006 1:36:35 PM >>Subject: Re: [BioC] probe level annotation >> >>Hi Tao, >> >> >> >>I just checked netaffx, and I get the same as the hgu133aprobe and >> >>hgu133acdf show: >> >> >> >>CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense >> >>GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense >> >>TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense >> >>AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense >> >>TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense >> >>TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense >> >>TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense >> >>ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense >> >>TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense >> >>AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense >> >>TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense >> >>TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense >> >>GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense >> >>GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense >> >>TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense >> >>ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense >> >> >> >>No idea why you got something different. >> >> >> >>Best, >> >> >> >>Jim >> >> >> >> >> >> >> >> >> >> >> >>Shi, Tao wrote: >> >> >>>Hi list, >> >>>I found the XY coordinates for the probes in 'hgu133aprobe' are not >> >>exactly the same as those shown on NetAffx.com. Please see below. >> >> >>>Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for >> >>examples, the same as in 'hgu133aprobe'? >> >> >>>thanks, >> >>>...Tao >> >>>>R.Version() >> >>>$platform >> >>>[1] "i386-pc-mingw32" >> >>>$arch >> >>>[1] "i386" >> >>>$os >> >>>[1] "mingw32" >> >>>$system >> >>>[1] "i386, mingw32" >> >>>$status >> >>>[1] "" >> >>>$major >> >>>[1] "2" >> >>>$minor >> >>>[1] "3.0" >> >>>$year >> >>>[1] "2006" >> >>>$month >> >>>[1] "04" >> >>>$day >> >>>[1] "24" >> >>>$`svn rev` >> >>>[1] "37909" >> >>>$language >> >>>[1] "R" >> >>>$version.string >> >>>[1] "Version 2.3.0 (2006-04-24)" >> >>>>library(hgu133aprobe) >> >>>>data(hgu133aprobe) >> >>>>as.data.frame(hgu133aprobe[1:16,]) >> >>> sequence x y Probe.Set.Name >> >>Probe.Interrogation.Position Target.Strandedness >> >> >>>1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at >> >> 3330 Antisense >> >> >>>2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at >> >> 3443 Antisense >> >> >>>3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at >> >> 3512 Antisense >> >> >>>4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at >> >> 3563 Antisense >> >> >>>5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at >> >> 3570 Antisense >> >> >>>6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at >> >> 3576 Antisense >> >> >>>7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at >> >> 3583 Antisense >> >> >>>8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at >> >> 3589 Antisense >> >> >>>9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at >> >> 3615 Antisense >> >> >>>10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at >> >> 3713 Antisense >> >> >>>11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at >> >> 3786 Antisense >> >> >>>12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at >> >> 3793 Antisense >> >> >>>13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at >> >> 3799 Antisense >> >> >>>14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at >> >> 3807 Antisense >> >> >>>15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at >> >> 3871 Antisense >> >> >>>16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at >> >> 3878 Antisense >> >> >>>>package.version('hgu133aprobe') >> >>>[1] "1.12.0" >> >>>And from NetAffx.com >> >>>Probe Sequence(5'-3') Probe X Probe Y Probe >> >>Interrogation >> >> >>>Position Target Strandedness >> >>>CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense >> >>>GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense >> >>>TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense >> >>>AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense >> >>>TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense >> >>>TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense >> >>>TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense >> >>>ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense >> >>>TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense >> >>>AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense >> >>>TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense >> >>>TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense >> >>>GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense >> >>>GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense >> >>>TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense >> >>>ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense >> >>>_______________________________________________ >> >>>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 >> >> >> >> >> >>-- >> >>James W. MacDonald, M.S. >> >>Biostatistician >> >>Affymetrix and cDNA Microarray Core >> >>University of Michigan Cancer Center >> >>1500 E. Medical Center Drive >> >>7410 CCGC >> >>Ann Arbor MI 48109 >> >>734-647-5623 >> >> >> >> >> >>********************************************************** >> >>Electronic Mail is not secure, may not be read every day, and should not >>be used for urgent or sensitive issues. >> >>_______________________________________________ >>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 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Shi, Tao ▴ 720
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Last seen 8.8 years ago
Hi Holger, If that's the case, how do you match them up? Thanks, ...Tao ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ Hi Tao, at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and pm(...) slightly differ. Best, Holger -------- Original-Nachricht -------- Datum: Mon, 2 Oct 2006 13:53:00 -0700 (PDT) Von: "Shi, Tao" <shidaxia at="" yahoo.com=""> An: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> Betreff: Re: [BioC] probe level annotation > Hi Jim, > > Thanks! My bad. I accidentally selected the HT 133A array. > > Any idea on my second question? I assume they are listed in the same > order, but not sure whether it's right. > > ...Tao > > > > > ----- Original Message ---- > From: James W. MacDonald <jmacdon at="" med.umich.edu=""> > To: "Shi, Tao" <shidaxia at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Monday, October 2, 2006 1:36:35 PM > Subject: Re: [BioC] probe level annotation > > Hi Tao, > > > > I just checked netaffx, and I get the same as the hgu133aprobe and > > hgu133acdf show: > > > > CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense > > GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense > > TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense > > AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense > > TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense > > TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense > > TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense > > ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense > > TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense > > AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense > > TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense > > TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense > > GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense > > GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense > > TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense > > ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense > > > > No idea why you got something different. > > > > Best, > > > > Jim > > > > > > > > > > > > Shi, Tao wrote: > > > Hi list, > > > > > > I found the XY coordinates for the probes in 'hgu133aprobe' are not > exactly the same as those shown on NetAffx.com. Please see below. > > > > > > Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for > examples, the same as in 'hgu133aprobe'? > > > > > > thanks, > > > > > > ...Tao > > > > > > > > > > > >>R.Version() > > > > > > $platform > > > [1] "i386-pc-mingw32" > > > > > > $arch > > > [1] "i386" > > > > > > $os > > > [1] "mingw32" > > > > > > $system > > > [1] "i386, mingw32" > > > > > > $status > > > [1] "" > > > > > > $major > > > [1] "2" > > > > > > $minor > > > [1] "3.0" > > > > > > $year > > > [1] "2006" > > > > > > $month > > > [1] "04" > > > > > > $day > > > [1] "24" > > > > > > $`svn rev` > > > [1] "37909" > > > > > > $language > > > [1] "R" > > > > > > $version.string > > > [1] "Version 2.3.0 (2006-04-24)" > > > > > > > > >>library(hgu133aprobe) > > >>data(hgu133aprobe) > > >>as.data.frame(hgu133aprobe[1:16,]) > > > > > > sequence x y Probe.Set.Name > Probe.Interrogation.Position Target.Strandedness > > > 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at > 3330 Antisense > > > 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at > 3443 Antisense > > > 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at > 3512 Antisense > > > 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at > 3563 Antisense > > > 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at > 3570 Antisense > > > 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at > 3576 Antisense > > > 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at > 3583 Antisense > > > 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at > 3589 Antisense > > > 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at > 3615 Antisense > > > 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at > 3713 Antisense > > > 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at > 3786 Antisense > > > 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at > 3793 Antisense > > > 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at > 3799 Antisense > > > 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at > 3807 Antisense > > > 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at > 3871 Antisense > > > 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at > 3878 Antisense > > > > > >>package.version('hgu133aprobe') > > > > > > [1] "1.12.0" > > > > > > > > > And from NetAffx.com > > > > > > Probe Sequence(5'-3') Probe X Probe Y Probe > Interrogation > > > Position Target Strandedness > > > CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense > > > GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense > > > TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense > > > AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense > > > TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense > > > TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense > > > TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense > > > ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense > > > TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense > > > AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense > > > TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense > > > TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense > > > GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense > > > GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense > > > TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense > > > ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense > > > > > > _______________________________________________ > > > 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 > > > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > 734-647-5623 > > > > > > ********************************************************** > > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues. > > _______________________________________________ > 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 --
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Hi Tao, using the x and the y coordinates in the annotation file, i.e., e.g., hgu133plus2probe$x and hgu133plus2probe$y, and the functions xy2indices and pmindex. Let tmp be an Affybatch object, and NR the number of rows on the chip (for the Plus2 chip, NR=1,164). Then something like > pI<-unlist(pmindex(tmp)) > mat.xy<-cbind(x=hgu133plus2probe$x,y=hgu133plus2probe$y) > ids.probes<-xy2indices(mat.xy,nr=NR) > match(ids.probes,pI) should work. Best, Holger -------- Original-Nachricht -------- Datum: Mon, 2 Oct 2006 14:08:13 -0700 (PDT) Von: "Shi, Tao" <shidaxia at="" yahoo.com=""> An: bioconductor at stat.math.ethz.ch Betreff: probe level annotation > Hi Holger, > > If that's the case, how do you match them up? Thanks, > > ...Tao > > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++ > Hi Tao, > > at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and > pm(...) slightly differ. > > Best, > Holger > > > -------- Original-Nachricht -------- > Datum: Mon, 2 Oct 2006 13:53:00 -0700 (PDT) > Von: "Shi, Tao" <shidaxia at="" yahoo.com=""> > An: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > Betreff: Re: [BioC] probe level annotation > > > Hi Jim, > > > > Thanks! My bad. I accidentally selected the HT 133A array. > > > > Any idea on my second question? I assume they are listed in the same > > order, but not sure whether it's right. > > > > ...Tao > > > > > > > > > > ----- Original Message ---- > > From: James W. MacDonald <jmacdon at="" med.umich.edu=""> > > To: "Shi, Tao" <shidaxia at="" yahoo.com=""> > > Cc: bioconductor at stat.math.ethz.ch > > Sent: Monday, October 2, 2006 1:36:35 PM > > Subject: Re: [BioC] probe level annotation > > > > Hi Tao, > > > > > > > > I just checked netaffx, and I get the same as the hgu133aprobe and > > > > hgu133acdf show: > > > > > > > > CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense > > > > GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense > > > > TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense > > > > AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense > > > > TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense > > > > TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense > > > > TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense > > > > ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense > > > > TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense > > > > AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense > > > > TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense > > > > TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense > > > > GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense > > > > GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense > > > > TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense > > > > ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense > > > > > > > > No idea why you got something different. > > > > > > > > Best, > > > > > > > > Jim > > > > > > > > > > > > > > > > > > > > > > > > Shi, Tao wrote: > > > > > Hi list, > > > > > > > > > > I found the XY coordinates for the probes in 'hgu133aprobe' are not > > exactly the same as those shown on NetAffx.com. Please see below. > > > > > > > > > > Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for > > examples, the same as in 'hgu133aprobe'? > > > > > > > > > > thanks, > > > > > > > > > > ...Tao > > > > > > > > > > > > > > > > > > > >>R.Version() > > > > > > > > > > $platform > > > > > [1] "i386-pc-mingw32" > > > > > > > > > > $arch > > > > > [1] "i386" > > > > > > > > > > $os > > > > > [1] "mingw32" > > > > > > > > > > $system > > > > > [1] "i386, mingw32" > > > > > > > > > > $status > > > > > [1] "" > > > > > > > > > > $major > > > > > [1] "2" > > > > > > > > > > $minor > > > > > [1] "3.0" > > > > > > > > > > $year > > > > > [1] "2006" > > > > > > > > > > $month > > > > > [1] "04" > > > > > > > > > > $day > > > > > [1] "24" > > > > > > > > > > $`svn rev` > > > > > [1] "37909" > > > > > > > > > > $language > > > > > [1] "R" > > > > > > > > > > $version.string > > > > > [1] "Version 2.3.0 (2006-04-24)" > > > > > > > > > > > > > > >>library(hgu133aprobe) > > > > >>data(hgu133aprobe) > > > > >>as.data.frame(hgu133aprobe[1:16,]) > > > > > > > > > > sequence x y Probe.Set.Name > > Probe.Interrogation.Position Target.Strandedness > > > > > 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at > > > 3330 Antisense > > > > > 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at > > > 3443 Antisense > > > > > 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at > > > 3512 Antisense > > > > > 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at > > > 3563 Antisense > > > > > 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at > > > 3570 Antisense > > > > > 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at > > > 3576 Antisense > > > > > 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at > > > 3583 Antisense > > > > > 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at > > > 3589 Antisense > > > > > 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at > > > 3615 Antisense > > > > > 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at > > > 3713 Antisense > > > > > 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at > > > 3786 Antisense > > > > > 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at > > > 3793 Antisense > > > > > 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at > > > 3799 Antisense > > > > > 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at > > > 3807 Antisense > > > > > 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at > > > 3871 Antisense > > > > > 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at > > > 3878 Antisense > > > > > > > > > >>package.version('hgu133aprobe') > > > > > > > > > > [1] "1.12.0" > > > > > > > > > > > > > > > And from NetAffx.com > > > > > > > > > > Probe Sequence(5'-3') Probe X Probe Y Probe > > Interrogation > > > > > Position Target Strandedness > > > > > CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense > > > > > GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense > > > > > TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense > > > > > AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense > > > > > TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense > > > > > TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense > > > > > TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense > > > > > ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense > > > > > TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense > > > > > AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense > > > > > TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense > > > > > TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense > > > > > GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense > > > > > GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense > > > > > TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense > > > > > ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > > > > -- > > > > James W. MacDonald, M.S. > > > > Biostatistician > > > > Affymetrix and cDNA Microarray Core > > > > University of Michigan Cancer Center > > > > 1500 E. Medical Center Drive > > > > 7410 CCGC > > > > Ann Arbor MI 48109 > > > > 734-647-5623 > > > > > > > > > > > > ********************************************************** > > > > Electronic Mail is not secure, may not be read every day, and should not > > be used for urgent or sensitive issues. > > > > _______________________________________________ > > 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 > > -- > > > --
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@james-w-macdonald-5106
Last seen 13 hours ago
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Hi Tao, I just checked netaffx, and I get the same as the hgu133aprobe and hgu133acdf show: CACCCAGCTGGTCCTGTGGATGGGA 467 181 3330 Antisense GCCCCACTGGACAACACTGATTCCT 531 299 3443 Antisense TGGACCCCACTGGCTGAGAATCTGG 86 557 3512 Antisense AAATGTTTCCTTGTGCCTGCTCCTG 365 115 3563 Antisense TCCTTGTGCCTGCTCCTGTACTTGT 207 605 3570 Antisense TGCCTGCTCCTGTACTTGTCCTCAG 593 599 3576 Antisense TCCTGTACTTGTCCTCAGCTTGGGC 425 607 3583 Antisense ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 3589 Antisense TCCTCCATCACCTGAAACACTGGAC 680 607 3615 Antisense AAGCCTATACGTTTCTGTGGAGTAA 532 139 3713 Antisense TTGGACATCTCTAGTGTAGCTGCCA 143 709 3786 Antisense TCTCTAGTGTAGCTGCCACATTGAT 285 623 3793 Antisense GTGTAGCTGCCACATTGATTTTTCT 383 479 3799 Antisense GCCACATTGATTTTTCTATAATCAC 129 279 3807 Antisense TACACTAATATATGGACCTAGCTTG 62 651 3871 Antisense ATATATGGACCTAGCTTGAGGCAAT 308 15 3878 Antisense No idea why you got something different. Best, Jim Shi, Tao wrote: > Hi list, > > I found the XY coordinates for the probes in 'hgu133aprobe' are not exactly the same as those shown on NetAffx.com. Please see below. > > Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for examples, the same as in 'hgu133aprobe'? > > thanks, > > ...Tao > > > >>R.Version() > > $platform > [1] "i386-pc-mingw32" > > $arch > [1] "i386" > > $os > [1] "mingw32" > > $system > [1] "i386, mingw32" > > $status > [1] "" > > $major > [1] "2" > > $minor > [1] "3.0" > > $year > [1] "2006" > > $month > [1] "04" > > $day > [1] "24" > > $`svn rev` > [1] "37909" > > $language > [1] "R" > > $version.string > [1] "Version 2.3.0 (2006-04-24)" > > >>library(hgu133aprobe) >>data(hgu133aprobe) >>as.data.frame(hgu133aprobe[1:16,]) > > sequence x y Probe.Set.Name Probe.Interrogation.Position Target.Strandedness > 1 CACCCAGCTGGTCCTGTGGATGGGA 467 181 1007_s_at 3330 Antisense > 2 GCCCCACTGGACAACACTGATTCCT 531 299 1007_s_at 3443 Antisense > 3 TGGACCCCACTGGCTGAGAATCTGG 86 557 1007_s_at 3512 Antisense > 4 AAATGTTTCCTTGTGCCTGCTCCTG 365 115 1007_s_at 3563 Antisense > 5 TCCTTGTGCCTGCTCCTGTACTTGT 207 605 1007_s_at 3570 Antisense > 6 TGCCTGCTCCTGTACTTGTCCTCAG 593 599 1007_s_at 3576 Antisense > 7 TCCTGTACTTGTCCTCAGCTTGGGC 425 607 1007_s_at 3583 Antisense > 8 ACTTGTCCTCAGCTTGGGCTTCTTC 552 101 1007_s_at 3589 Antisense > 9 TCCTCCATCACCTGAAACACTGGAC 680 607 1007_s_at 3615 Antisense > 10 AAGCCTATACGTTTCTGTGGAGTAA 532 139 1007_s_at 3713 Antisense > 11 TTGGACATCTCTAGTGTAGCTGCCA 143 709 1007_s_at 3786 Antisense > 12 TCTCTAGTGTAGCTGCCACATTGAT 285 623 1007_s_at 3793 Antisense > 13 GTGTAGCTGCCACATTGATTTTTCT 383 479 1007_s_at 3799 Antisense > 14 GCCACATTGATTTTTCTATAATCAC 129 279 1007_s_at 3807 Antisense > 15 TACACTAATATATGGACCTAGCTTG 62 651 1007_s_at 3871 Antisense > 16 ATATATGGACCTAGCTTGAGGCAAT 308 15 1007_s_at 3878 Antisense > >>package.version('hgu133aprobe') > > [1] "1.12.0" > > > And from NetAffx.com > > Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation > Position Target Strandedness > CACCCAGCTGGTCCTGTGGATGGGA 197 207 3330 Antisense > GCCCCACTGGACAACACTGATTCCT 592 319 3443 Antisense > TGGACCCCACTGGCTGAGAATCTGG 85 591 3512 Antisense > AAATGTTTCCTTGTGCCTGCTCCTG 559 139 3563 Antisense > TCCTTGTGCCTGCTCCTGTACTTGT 269 633 3570 Antisense > TGCCTGCTCCTGTACTTGTCCTCAG 378 629 3576 Antisense > TCCTGTACTTGTCCTCAGCTTGGGC 536 643 3583 Antisense > ACTTGTCCTCAGCTTGGGCTTCTTC 479 125 3589 Antisense > TCCTCCATCACCTGAAACACTGGAC 575 643 3615 Antisense > AAGCCTATACGTTTCTGTGGAGTAA 497 161 3713 Antisense > TTGGACATCTCTAGTGTAGCTGCCA 635 739 3786 Antisense > TCTCTAGTGTAGCTGCCACATTGAT 74 659 3793 Antisense > GTGTAGCTGCCACATTGATTTTTCT 660 503 3799 Antisense > GCCACATTGATTTTTCTATAATCAC 80 313 3807 Antisense > TACACTAATATATGGACCTAGCTTG 739 685 3871 Antisense > ATATATGGACCTAGCTTGAGGCAAT 242 31 3878 Antisense > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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