Hello I have had to review recently an analysis I did some time ago. This was done on affymetrix hgu133plus2 chips with R 2.4 and BioC 1.9 I have re-run the analyses using R 2.9 and BioC 2.4 (sessionInfo below). I have been surprised by the changes in the annotations: Many probesets that had had an annotation have become NA's whereas some have changed their symbol and their Entrez gene. To be specific I summarize my question with the top genes of my list The list I obtained 2 years ago is: probeset locuslink symbol 238900_at 3123 HLA-DRB1 232583_at 8440 NCK2 236307_at 60468 BACH2 223620_at 2857 GPR34 219759_at 64167 LRAP 201702_s_at 5514 PPP1R10 232882_at 2308 FOXO1A 213446_s_at 8826 IQGAP1 234033_at 9693 RAPGEF2 243006_at 2534 FYN 244648_at 54520 CCDC93 243691_at 23142 DCUN1D4 239264_at 60412 EXOC4 243546_at 143686 SESN3 205239_at 374 AREG 1565703_at 55520 ELAC1 244061_at 55843 ARHGAP15 230505_at 26037 SIPA1L1 242688_at 9320 TRIP12 1556474_a_at 285097 FLJ38379 232614_at 596 BCL2 1565689_at 3839 KPNA3 236685_at NA NA 225173_at 93663 ARHGAP18 241893_at 4249 MGAT5 I used the following code to reproduce the issue with the annotations: ##################################################################### ## Verification using R 2.9 & BioC 2.4 ##################################################################### > probes<-c("238900_at" , "232583_at", "236307_at" ,"223620_at" , "219759_at" , + "201702_s_at" , "232882_at" , "213446_s_at", "234033_at", "243006_at" , + "244648_at" , "243691_at" , "239264_at" , "243546_at" , "205239_at" , + "1565703_at" , "244061_at" , "230505_at" , "242688_at" , "1556474_a_at", + "232614_at" , "1565689_at" , "236685_at" , "225173_at" , "241893_at") > > library(hgu133plus2.db) > library(annotate) > > entrezs<- getEG(probes, "hgu133plus2") > symbols<- getSYMBOL(probes, "hgu133plus2") > sel2<- cbind(probes, entrezs, symbols) > sel2 probes entrezs symbols 238900_at "238900_at" "100133484" "LOC100133484" 232583_at "232583_at" NA NA 236307_at "236307_at" NA NA 223620_at "223620_at" "2857" "GPR34" 219759_at "219759_at" "64167" "ERAP2" 201702_s_at "201702_s_at" "5514" "PPP1R10" 232882_at "232882_at" NA NA 213446_s_at "213446_s_at" "8826" "IQGAP1" 234033_at "234033_at" NA NA 243006_at "243006_at" NA NA 244648_at "244648_at" NA NA 243691_at "243691_at" NA NA 239264_at "239264_at" NA NA 243546_at "243546_at" NA NA 205239_at "205239_at" "374" "AREG" 1565703_at "1565703_at" "4089" "SMAD4" 244061_at "244061_at" NA NA 230505_at "230505_at" "145474" "LOC145474" 242688_at "242688_at" NA NA 1556474_a_at "1556474_a_at" "285097" "FLJ38379" 232614_at "232614_at" NA NA 1565689_at "1565689_at" NA NA 236685_at "236685_at" NA NA 225173_at "225173_at" "93663" "ARHGAP18" 241893_at "241893_at" NA NA > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.22.0 hgu133plus2.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] xtable_1.5-5 ############################################# Many probesets seem to have changed. Can someone explain to me what is happening (or what may I be doing wrong)? The same code does not work with R 2.4 but if I change hgu133plus2.db by hgu133plus2 and getEG by getLL I obtain the original results: ############################################### ### Review of annotatons with R 2.4 and BioC 1.9 ############################################### ### This code is executed on a clean new session with R 2. and BioC 1.9 > probes<-c("238900_at" , "232583_at", "236307_at" ,"223620_at" , "219759_at" , + "201702_s_at" , "232882_at" , "213446_s_at", "234033_at", "243006_at" , + "244648_at" , "243691_at" , "239264_at" , "243546_at" , "205239_at" , + "1565703_at" , "244061_at" , "230505_at" , "242688_at" , "1556474_a_at", + "232614_at" , "1565689_at" , "236685_at" , "225173_at" , "241893_at") > >LLs<- getLL(rownames(sel), "hgu133plus2") >symbols<- getSYMBOL(rownames(sel), "hgu133plus2") >sel1<- cbind(probes, LLs, symbols) >sel1 probes LLs symbols 238900_at "238900_at" "3123" "HLA-DRB1" 232583_at "232583_at" "8440" "NCK2" 236307_at "236307_at" "60468" "BACH2" 223620_at "223620_at" "2857" "GPR34" 219759_at "219759_at" "64167" "ERAP2" 201702_s_at "201702_s_at" "5514" "PPP1R10" 232882_at "232882_at" "2308" "FOXO1" 213446_s_at "213446_s_at" "8826" "IQGAP1" 234033_at "234033_at" "9693" "RAPGEF2" 243006_at "243006_at" "2534" "FYN" 244648_at "244648_at" "54520" "CCDC93" 243691_at "243691_at" "23142" "DCUN1D4" 239264_at "239264_at" "60412" "EXOC4" 243546_at "243546_at" "143686" "SESN3" 205239_at "205239_at" "374" "AREG" 1565703_at "1565703_at" "4089" "SMAD4" 244061_at "244061_at" "55843" "ARHGAP15" 230505_at "230505_at" "145474" "LOC145474" 242688_at "242688_at" "9320" "TRIP12" 1556474_a_at "1556474_a_at" "285097" "FLJ38379" 232614_at "232614_at" "596" "BCL2" 1565689_at "1565689_at" "3839" "KPNA3" 236685_at "236685_at" NA NA 225173_at "225173_at" "93663" "ARHGAP18" 241893_at "241893_at" "4249" "MGAT5" > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" [5] "utils" "datasets" "methods" "base" other attached packages: annotate Biobase hgu133plus2 "1.12.1" "1.12.2" "1.14.0" ######################################################## In summary. If I use R 2.4/BioC 1.9 I obtain the same results I ibtained 2 years ago, but If I do the same steps using R2.9/BioC2.4 the results change dramatically. I have repeated the analyses using BioC 2.01 in R 2.7 and BioC 2.2 in R 2.8 (results not shown here). BioC 2.0 yield the same as 1.9 and BioC 2.2 the same as 2.4, Any help to understand what's happening would be appreciated Alex Sanchez ----------------------------------------------------------------------------------------------------- Dr. Alex Sánchez. Statistics Department. University of Barcelona. Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain asanchez_at_ub.edu Statistics and Bioinformatics Unit Institut de Recerca. Hospital Universitari Vall 'Hebron Passeig Vall d'Hebron 112-119. 08034 Barcelona asanchez_at_ir.vhebron.net ---------------------------------------------------------------------------------------------------- [[alternative HTML version deleted]]