Hello bioconductor-help members, My apologies if this email has arrived in the wrong group. I read over the posting guide and I wasn't sure if this was the correct forum for this question -- if it is not, please let me know and I will remove this posting and resubmit to the correct group. Finally, apologies for the long post, but to reproduce this problem requires several steps. Step 1) Download a sample X_laevis_2 CEL file from Geo I choose the experiment GSM579981 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM579981 Clicking on the platform shows that it is a X_laevis_2 experiment http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10756 For our sample file, I choose GSM579981.CEL.gz You can download this file at this url: http://www.ncbi.nlm.nih.gov/geosuppl/?acc=GSM579981&file=GSM579981%2EC EL%2Egz Unzip the file prior to reading it in. Step 2) Read In the CEL File and verify that it is an X_laevis_2 chip > library(affy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > chipData<-ReadAffy("GSM579981.CEL") chipData > chipData AffyBatch object size of arrays=984x984 features (16 kb) cdf=X_laevis_2 (32635 affyids) number of samples=1 number of genes=32635 annotation=xlaevis2 notes= Step 3) Examine the Probes for the sample -- I jump directly into the middle of the list to examine some probe names > probes <- indexProbes(chipData,which="pm") > probes[10000:10003] $Xl.22397.1.S1_at [1] 28653 395253 596069 345939 37062 672483 385713 355738 658991 845464 [11] 215644 808173 660480 355294 $Xl.22404.1.S1_at [1] 751168 802621 258978 278901 770602 722241 468139 41006 622884 434793 [11] 552950 654955 717774 464009 $Xl.22404.2.A1_at [1] 403052 562419 290807 200686 31036 302164 198607 877595 238016 872893 [11] 151357 662822 465642 50403 $Xl.22413.2.S1_a_at [1] 776460 314189 678641 883234 210521 74592 808408 54975 857096 600001 [11] 298898 560070 544638 517362 Step 4) Map the probes back to the Affy Reference files Examining the probe data from GeneChip Xenopus laevis Genome 2.0 Array http://www.affymetrix.com/browse/products.jsp?productId=131525&navMode =34000&navAction=jump&aId=productsNav#1_1 These Xl.* probes are not in the affymetrix probe file: http://www.affymetrix.com/Auth/analysis/downloads/data/X_laevis_2.prob e_tab.zip (May require Registration) grep -n2 "Xl.22404." X_laevis_2.probe_tab < NOTHING FOUND > Instead, these probe names are actually in the Gen 1 -- GeneChip Xenopus laevis Genome Array http://www.affymetrix.com/esearch/search.jsp?pd=131526&N=4294967292 https://www.affymetrix.com/Auth/analysis/downloads/data/Xenopus_laevis .probe_fasta.zip (May require Registration) dsanphil01-2:Downloads pcheung$ grep -n2 "Xl.22404." Xenopus_laevis.probe_fasta 239203->probe:Xenopus_laevis:Xl.22388.1.S1_at:328:541; Interrogation_Position=756; Antisense; 239204-GGCCATGACTAGAGTCGTTCTTCCC 239205:>probe:Xenopus_laevis:Xl.22404.1.S1_at:212:39; Interrogation_Position=150; Antisense; 239206-ATCTGGCCCAAACCTTTTGAAACAG 239207:>probe:Xenopus_laevis:Xl.22404.1.S1_at:177:541; Interrogation_Position=153; Antisense; 239208-TGGCCCAAACCTTTTGAAACAGCAC 239209:>probe:Xenopus_laevis:Xl.22404.1.S1_at:171:151; Interrogation_Position=159; Antisense; 239210-AAACCTTTTGAAACAGCACCCGATG 239211:>probe:Xenopus_laevis:Xl.22404.1.S1_at:616:169; Interrogation_Position=160; Antisense; 239212-AACCTTTTGAAACAGCACCCGATGC 239213:>probe:Xenopus_laevis:Xl.22404.1.S1_at:630:109; Interrogation_Position=161; Antisense; 239214-ACCTTTTGAAACAGCACCCGATGCA 239215:>probe:Xenopus_laevis:Xl.22404.1.S1_at:543:671; Interrogation_Position=164; Antisense; 239216-TTTTGAAACAGCACCCGATGCACTC 239217:>probe:Xenopus_laevis:Xl.22404.1.S1_at:365:659; Interrogation_Position=165; Antisense; 239218-TTTGAAACAGCACCCGATGCACTCC 239219:>probe:Xenopus_laevis:Xl.22404.1.S1_at:141:105; Interrogation_Position=176; Antisense; 239220-ACCCGATGCACTCCAGCTTTGCTGG 239221:>probe:Xenopus_laevis:Xl.22404.1.S1_at:271:273; Interrogation_Position=178; Antisense; 239222-CCGATGCACTCCAGCTTTGCTGGTT 239223:>probe:Xenopus_laevis:Xl.22404.1.S1_at:126:299; Interrogation_Position=43; Antisense; 239224-GCGGAGGGCTGTTCATGTTGCATAT 239225:>probe:Xenopus_laevis:Xl.22404.1.S1_at:105:267; Interrogation_Position=44; Antisense; 239226-CGGAGGGCTGTTCATGTTGCATATT 239227:>probe:Xenopus_laevis:Xl.22404.1.S1_at:395:517; Interrogation_Position=45; Antisense; 239228-GGAGGGCTGTTCATGTTGCATATTG 239229:>probe:Xenopus_laevis:Xl.22404.1.S1_at:128:71; Interrogation_Position=47; Antisense; 239230-AGGGCTGTTCATGTTGCATATTGGA 239231:>probe:Xenopus_laevis:Xl.22404.1.S1_at:233:489; Interrogation_Position=48; Antisense; 239232-GGGCTGTTCATGTTGCATATTGGAA 239233:>probe:Xenopus_laevis:Xl.22404.1.S1_at:239:301; Interrogation_Position=50; Antisense; 239234-GCTGTTCATGTTGCATATTGGAATT 239235:>probe:Xenopus_laevis:Xl.22404.1.S1_at:389:445; Interrogation_Position=85; Antisense; 239236-GTAGGGTGCATAATATGCACAAGTC 239237->probe:Xenopus_laevis:Xl.22710.1.S1_at:596:377; Interrogation_Position=1190; Antisense;

Hi Philip, On 11/12/2012 3:42 PM, Philip Cheung wrote: > Hello bioconductor-help members, > > My apologies if this email has arrived in the wrong group. I read > over the posting guide and I wasn't sure if this was the correct forum > for this question -- if it is not, please let me know and I will > remove this posting and resubmit to the correct group. > > Finally, apologies for the long post, but to reproduce this problem > requires several steps. Actually it doesn't take any of those steps. library(BiocInstaller) biocLite(c("xlaevis2cdf","xlaevis2probe")) library(xlaevis2cdf) library(xlaevis2probe) x <- ls(xlaevis2cdf) y <- unique(as.character(xlaevis2probe$Probe.Set.Name)) sum(x %in% y) 160 length(x) 32635 So yeah. It appears the xlaevis2 cdf that I have been using is an older version, which contains lots of probesets with an Xl.xxx instead of the current version which has probesets like Xl2.xxx. I have sent the corrected version to Marc Carlson, who is in charge of getting such things on the website and available to download. I assume this will happen in the next few days. Thanks for pointing that out! Best, Jim > > Step 1) Download a sample X_laevis_2 CEL file from Geo > > I choose the experiment GSM579981 > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM579981 > > Clicking on the platform shows that it is a X_laevis_2 experiment > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10756 > > For our sample file, I choose GSM579981.CEL.gz > > You can download this file at this url: > http://www.ncbi.nlm.nih.gov/geosuppl/?acc=GSM579981&file=GSM579981%2 ECEL%2Egz > > Unzip the file prior to reading it in. > > > Step 2) Read In the CEL File and verify that it is an X_laevis_2 chip > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> chipData<-ReadAffy("GSM579981.CEL") > chipData >> chipData > AffyBatch object > size of arrays=984x984 features (16 kb) > cdf=X_laevis_2 (32635 affyids) > number of samples=1 > number of genes=32635 > annotation=xlaevis2 > notes= > > > Step 3) Examine the Probes for the sample -- I jump directly into the > middle of the list to examine some probe names > >> probes<- indexProbes(chipData,which="pm") >> probes[10000:10003] > $Xl.22397.1.S1_at > [1] 28653 395253 596069 345939 37062 672483 385713 355738 658991 845464 > [11] 215644 808173 660480 355294 > > $Xl.22404.1.S1_at > [1] 751168 802621 258978 278901 770602 722241 468139 41006 622884 434793 > [11] 552950 654955 717774 464009 > > $Xl.22404.2.A1_at > [1] 403052 562419 290807 200686 31036 302164 198607 877595 238016 872893 > [11] 151357 662822 465642 50403 > > $Xl.22413.2.S1_a_at > [1] 776460 314189 678641 883234 210521 74592 808408 54975 857096 600001 > [11] 298898 560070 544638 517362 > > > Step 4) Map the probes back to the Affy Reference files > > Examining the probe data from GeneChip Xenopus laevis Genome 2.0 Array > http://www.affymetrix.com/browse/products.jsp?productId=131525&navMo de=34000&navAction=jump&aId=productsNav#1_1 > > These Xl.* probes are not in the affymetrix probe file: > http://www.affymetrix.com/Auth/analysis/downloads/data/X_laevis_2.pr obe_tab.zip > (May require Registration) > > grep -n2 "Xl.22404." X_laevis_2.probe_tab > > < NOTHING FOUND> > > > > Instead, these probe names are actually in the Gen 1 -- GeneChip > Xenopus laevis Genome Array > http://www.affymetrix.com/esearch/search.jsp?pd=131526&N=4294967292 > > > https://www.affymetrix.com/Auth/analysis/downloads/data/Xenopus_laev is.probe_fasta.zip > (May require Registration) > > > dsanphil01-2:Downloads pcheung$ grep -n2 "Xl.22404." Xenopus_laevis.probe_fasta > 239203->probe:Xenopus_laevis:Xl.22388.1.S1_at:328:541; > Interrogation_Position=756; Antisense; > 239204-GGCCATGACTAGAGTCGTTCTTCCC > 239205:>probe:Xenopus_laevis:Xl.22404.1.S1_at:212:39; > Interrogation_Position=150; Antisense; > 239206-ATCTGGCCCAAACCTTTTGAAACAG > 239207:>probe:Xenopus_laevis:Xl.22404.1.S1_at:177:541; > Interrogation_Position=153; Antisense; > 239208-TGGCCCAAACCTTTTGAAACAGCAC > 239209:>probe:Xenopus_laevis:Xl.22404.1.S1_at:171:151; > Interrogation_Position=159; Antisense; > 239210-AAACCTTTTGAAACAGCACCCGATG > 239211:>probe:Xenopus_laevis:Xl.22404.1.S1_at:616:169; > Interrogation_Position=160; Antisense; > 239212-AACCTTTTGAAACAGCACCCGATGC > 239213:>probe:Xenopus_laevis:Xl.22404.1.S1_at:630:109; > Interrogation_Position=161; Antisense; > 239214-ACCTTTTGAAACAGCACCCGATGCA > 239215:>probe:Xenopus_laevis:Xl.22404.1.S1_at:543:671; > Interrogation_Position=164; Antisense; > 239216-TTTTGAAACAGCACCCGATGCACTC > 239217:>probe:Xenopus_laevis:Xl.22404.1.S1_at:365:659; > Interrogation_Position=165; Antisense; > 239218-TTTGAAACAGCACCCGATGCACTCC > 239219:>probe:Xenopus_laevis:Xl.22404.1.S1_at:141:105; > Interrogation_Position=176; Antisense; > 239220-ACCCGATGCACTCCAGCTTTGCTGG > 239221:>probe:Xenopus_laevis:Xl.22404.1.S1_at:271:273; > Interrogation_Position=178; Antisense; > 239222-CCGATGCACTCCAGCTTTGCTGGTT > 239223:>probe:Xenopus_laevis:Xl.22404.1.S1_at:126:299; > Interrogation_Position=43; Antisense; > 239224-GCGGAGGGCTGTTCATGTTGCATAT > 239225:>probe:Xenopus_laevis:Xl.22404.1.S1_at:105:267; > Interrogation_Position=44; Antisense; > 239226-CGGAGGGCTGTTCATGTTGCATATT > 239227:>probe:Xenopus_laevis:Xl.22404.1.S1_at:395:517; > Interrogation_Position=45; Antisense; > 239228-GGAGGGCTGTTCATGTTGCATATTG > 239229:>probe:Xenopus_laevis:Xl.22404.1.S1_at:128:71; > Interrogation_Position=47; Antisense; > 239230-AGGGCTGTTCATGTTGCATATTGGA > 239231:>probe:Xenopus_laevis:Xl.22404.1.S1_at:233:489; > Interrogation_Position=48; Antisense; > 239232-GGGCTGTTCATGTTGCATATTGGAA > 239233:>probe:Xenopus_laevis:Xl.22404.1.S1_at:239:301; > Interrogation_Position=50; Antisense; > 239234-GCTGTTCATGTTGCATATTGGAATT > 239235:>probe:Xenopus_laevis:Xl.22404.1.S1_at:389:445; > Interrogation_Position=85; Antisense; > 239236-GTAGGGTGCATAATATGCACAAGTC > 239237->probe:Xenopus_laevis:Xl.22710.1.S1_at:596:377; > Interrogation_Position=1190; Antisense; > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. 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