memory invalid permission with qc()
1
0
Entering edit mode
SimonNoël ▴ 450
@simonnoel-3455
Last seen 9.6 years ago
Hello. I have some problem using qc(). I have an old data set that work perfectly with qc() but a nuw one just arrive from affymetrix and I am not able to run qc() on it. I use the code : library(affy) library(affyio) library(simpleaffy) Data <-ReadAffy() qc <- qc(Data) and I recive this error message : *** caught segfault *** address 0xb6cf9000, cause 'invalid permissions' Traceback: 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, x]), as.character(pns), as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs = double(length(unique.pns)), length(unique.pns), PACKAGE = "simpleaffy") 2: FUN(1:2[[1L]], ...) 3: lapply(X, FUN, ...) 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, x]), as.character(pns), as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs = double(length(unique.pns)), length(unique.pns), PACKAGE = "simpleaffy")$exprs}) 5: justMAS(x, tgt = sc) 6: call.exprs(unnormalised, "mas5") 7: qc.affy(unnormalised, ...) 8: qc(Data) 9: qc(Data) 10: eval.with.vis(expr, envir, enclos) 11: eval.with.vis(ei, envir) 12: source("tmp.R") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: What should I do to correct the problem? Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
• 1.8k views
ADD COMMENT •
0
Entering edit mode
@wolfgang-huber-3550
Last seen 17 days ago
EMBL European Molecular Biology Laborat…
Simon No?l ha scritto: > Hello. I have some problem using qc(). I have an old data set that work > perfectly with qc() but a nuw one just arrive from affymetrix and I am not able > to run qc() on it. I use the code : > > library(affy) > > > > library(affyio) > > > library(simpleaffy) > > Data <-ReadAffy() > > qc <- qc(Data) > > and I recive this error message : > > *** caught segfault *** > address 0xb6cf9000, cause 'invalid permissions' > > Traceback: > 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, x]), > as.character(pns), as.integer(length(mms[, x])), as.double(ct), > as.double(st), exprs = double(length(unique.pns)), length(unique.pns), > PACKAGE = "simpleaffy") > 2: FUN(1:2[[1L]], ...) > 3: lapply(X, FUN, ...) > 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", > as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs = > double(length(unique.pns)), length(unique.pns), PACKAGE = > "simpleaffy")$exprs}) > 5: justMAS(x, tgt = sc) > 6: call.exprs(unnormalised, "mas5") > 7: qc.affy(unnormalised, ...) > 8: qc(Data) > 9: qc(Data) > 10: eval.with.vis(expr, envir, enclos) > 11: eval.with.vis(ei, envir) > 12: source("tmp.R") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > What should I do to correct the problem? > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC Dear Simon what is your "sessionInfo()"? Are you using the latest release of R (2.9) and Bioconductor? Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
ADD COMMENT •
0
Entering edit mode
My sessionInfo() is R version 2.8.1 (2008-12-22) i486-pc-linux-gnu locale: LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 genefilter_1.22.0 [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 [4] preprocessCore_1.4.0 RSQLite_0.7-1 For the relase, I am new to R and Bioconductor. I have started the 12 May... SO I think that I use the lastest. Is's the same thing with my computer OS. My first job was to install everything. I am newly out of school for the summer. Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > Simon No?l ha scritto: > > Hello. I have some problem using qc(). I have an old data set that work > > perfectly with qc() but a nuw one just arrive from affymetrix and I am not > able > > to run qc() on it. I use the code : > > > > library(affy) > > > > > > > > library(affyio) > > > > > > library(simpleaffy) > > > > Data <-ReadAffy() > > > > qc <- qc(Data) > > > > and I recive this error message : > > > > *** caught segfault *** > > address 0xb6cf9000, cause 'invalid permissions' > > > > Traceback: > > 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, x]), > > as.character(pns), as.integer(length(mms[, x])), as.double(ct), > > as.double(st), exprs = double(length(unique.pns)), length(unique.pns), > > PACKAGE = "simpleaffy") > > 2: FUN(1:2[[1L]], ...) > > 3: lapply(X, FUN, ...) > > 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", > > as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > > as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs = > > double(length(unique.pns)), length(unique.pns), PACKAGE = > > "simpleaffy")$exprs}) > > 5: justMAS(x, tgt = sc) > > 6: call.exprs(unnormalised, "mas5") > > 7: qc.affy(unnormalised, ...) > > 8: qc(Data) > > 9: qc(Data) > > 10: eval.with.vis(expr, envir, enclos) > > 11: eval.with.vis(ei, envir) > > 12: source("tmp.R") > > > > Possible actions: > > 1: abort (with core dump, if enabled) > > 2: normal R exit > > 3: exit R without saving workspace > > 4: exit R saving workspace > > Selection: > > > > What should I do to correct the problem? > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > Dear Simon > > what is your "sessionInfo()"? > > Are you using the latest release of R (2.9) and Bioconductor? > > Best wishes > Wolfgang > > ------------------------------------------------ > Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Hi Simon, Simon No?l wrote: > My sessionInfo() is > > R version 2.8.1 (2008-12-22) > i486-pc-linux-gnu > > locale: > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_ CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 genefilter_1.22.0 > [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 > [4] preprocessCore_1.4.0 RSQLite_0.7-1 > > For the relase, I am new to R and Bioconductor. I have started the 12 May... > SO I think that I use the lastest. Is's the same thing with my computer OS. > My first job was to install everything. I am newly out of school for the > summer. Actually, you have an old version of R and BioC. You want to upgrade to R-2.9.0 and BioC 2.4 and then see if you still have the same problem Best, Jim > > > > Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > >> Simon No?l ha scritto: >>> Hello. I have some problem using qc(). I have an old data set that work >>> perfectly with qc() but a nuw one just arrive from affymetrix and I am not >> able >>> to run qc() on it. I use the code : >>> >>> library(affy) >>> >>> >>> >>> library(affyio) >>> >>> >>> library(simpleaffy) >>> >>> Data <-ReadAffy() >>> >>> qc <- qc(Data) >>> >>> and I recive this error message : >>> >>> *** caught segfault *** >>> address 0xb6cf9000, cause 'invalid permissions' >>> >>> Traceback: >>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, x]), >>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), >>> as.double(st), exprs = double(length(unique.pns)), length(unique.pns), >>> PACKAGE = "simpleaffy") >>> 2: FUN(1:2[[1L]], ...) >>> 3: lapply(X, FUN, ...) >>> 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", >>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), >>> as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs = >>> double(length(unique.pns)), length(unique.pns), PACKAGE = >>> "simpleaffy")$exprs}) >>> 5: justMAS(x, tgt = sc) >>> 6: call.exprs(unnormalised, "mas5") >>> 7: qc.affy(unnormalised, ...) >>> 8: qc(Data) >>> 9: qc(Data) >>> 10: eval.with.vis(expr, envir, enclos) >>> 11: eval.with.vis(ei, envir) >>> 12: source("tmp.R") >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> Selection: >>> >>> What should I do to correct the problem? >>> >>> Simon No?l >>> VP Externe CADEUL >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>> informatique et Microbiologie de l'Universit? Laval >>> CdeC >> >> >> Dear Simon >> >> what is your "sessionInfo()"? >> >> Are you using the latest release of R (2.9) and Bioconductor? >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------ >> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber >> >> > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLY •
0
Entering edit mode
Hello. I think that every thing is updated now. I still get the error. My new sessionInfo() is R version 2.9.0 (2009-04-17) i486-pc-linux-gnu locale: LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > Hi Simon, > > Simon No?l wrote: > > My sessionInfo() is > > > > R version 2.8.1 (2008-12-22) > > i486-pc-linux-gnu > > > > locale: > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > > [8] methods base > > > > other attached packages: > > [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > genefilter_1.22.0 > > [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 Biobase_2.2.2 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 > > [4] preprocessCore_1.4.0 RSQLite_0.7-1 > > > > For the relase, I am new to R and Bioconductor. I have started the 12 > May... > > SO I think that I use the lastest. Is's the same thing with my computer > OS. > > My first job was to install everything. I am newly out of school for the > > summer. > > Actually, you have an old version of R and BioC. You want to upgrade to > R-2.9.0 and BioC 2.4 and then see if you still have the same problem > > Best, > > Jim > > > > > > > > > > Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > > > >> Simon No?l ha scritto: > >>> Hello. I have some problem using qc(). I have an old data set that work > >>> perfectly with qc() but a nuw one just arrive from affymetrix and I am > not > >> able > >>> to run qc() on it. I use the code : > >>> > >>> library(affy) > >>> > >>> > >>> > >>> library(affyio) > >>> > >>> > >>> library(simpleaffy) > >>> > >>> Data <-ReadAffy() > >>> > >>> qc <- qc(Data) > >>> > >>> and I recive this error message : > >>> > >>> *** caught segfault *** > >>> address 0xb6cf9000, cause 'invalid permissions' > >>> > >>> Traceback: > >>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, > x]), > >>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), > >>> as.double(st), exprs = double(length(unique.pns)), length(unique.pns), > >>> PACKAGE = "simpleaffy") > >>> 2: FUN(1:2[[1L]], ...) > >>> 3: lapply(X, FUN, ...) > >>> 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", > >>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > >>> as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs > = > >>> double(length(unique.pns)), length(unique.pns), PACKAGE = > >>> "simpleaffy")$exprs}) > >>> 5: justMAS(x, tgt = sc) > >>> 6: call.exprs(unnormalised, "mas5") > >>> 7: qc.affy(unnormalised, ...) > >>> 8: qc(Data) > >>> 9: qc(Data) > >>> 10: eval.with.vis(expr, envir, enclos) > >>> 11: eval.with.vis(ei, envir) > >>> 12: source("tmp.R") > >>> > >>> Possible actions: > >>> 1: abort (with core dump, if enabled) > >>> 2: normal R exit > >>> 3: exit R without saving workspace > >>> 4: exit R saving workspace > >>> Selection: > >>> > >>> What should I do to correct the problem? > >>> > >>> Simon No?l > >>> VP Externe CADEUL > >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>> informatique et Microbiologie de l'Universit? Laval > >>> CdeC > >> > >> > >> Dear Simon > >> > >> what is your "sessionInfo()"? > >> > >> Are you using the latest release of R (2.9) and Bioconductor? > >> > >> Best wishes > >> Wolfgang > >> > >> ------------------------------------------------ > >> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > >> > >> > > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > _______________________________________________ > > 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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Weird. What kind of chip? Does this work for you? library(simpleaffy) library(affydata) data(Dilution) qc(Dilution) I get > qc(Dilution) An object of class "QCStats" Slot "scale.factors": [1] 0.8934013 1.2653627 1.1448430 1.8454067 Slot "target": [1] 100 Slot "percent.present": 20A.present 20B.present 10A.present 10B.present 48.79208 49.82178 49.37822 49.75842 Slot "average.background": 20A 20B 10A 10B 94.25323 63.63855 80.09436 54.25830 Slot "minimum.background": 20A 20B 10A 10B 89.52555 60.01397 77.32196 49.22574 Slot "maximum.background": 20A 20B 10A 10B 97.66280 68.18998 83.24646 57.62283 Slot "spikes": AFFX-BioB-3_at AFFX-BioC-3_at AFFX-BioDn-3_at AFFX-CreX-3_at 20A 11.64085 7.979776 11.92078 7.879601 20B 11.23099 7.682558 11.72899 7.752151 10A 11.89294 8.191754 12.20780 7.888115 10B 12.18343 8.644352 12.50579 8.357746 Slot "qc.probes": AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at AFFX- HSAC07/X00351_M_at 20A 12.43699 11.74085 12.30966 20B 12.29240 11.57156 12.11278 10A 12.78294 11.91173 12.57164 10B 12.70788 11.77651 12.43533 AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at 20A 12.12079 11.67781 20B 11.95684 11.60385 10A 12.26970 11.83704 10B 12.30909 11.73642 AFFX-HUMGAPDH/M33197_M_at 20A 12.18103 20B 11.97050 10A 11.84595 10B 12.19650 Slot "bioBCalls": 20A.present 20B.present 10A.present 10B.present "P" "P" "P" "P" Slot "arraytype": [1] "hgu95av2cdf" > 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 datasets utils methods base other attached packages: [1] hgu95av2cdf_2.4.0 affydata_1.11.5 simpleaffy_2.20.0 gcrma_2.15.5 [5] Biostrings_2.11.53 IRanges_1.1.66 genefilter_1.23.4 affy_1.21.10 [9] Biobase_2.3.11 loaded via a namespace (and not attached): [1] affyio_1.11.3 annotate_1.21.5 AnnotationDbi_1.5.23 [4] DBI_0.2-4 preprocessCore_1.5.3 RSQLite_0.7-1 [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 [10] xtable_1.5-5 > Simon No?l wrote: > Hello. I think that every thing is updated now. I still get the error. > > My new sessionInfo() is > > R version 2.9.0 (2009-04-17) > i486-pc-linux-gnu > > locale: > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_ CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 > [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 > [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 > [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 > > > > > Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > >> Hi Simon, >> >> Simon No?l wrote: >>> My sessionInfo() is >>> >>> R version 2.8.1 (2008-12-22) >>> i486-pc-linux-gnu >>> >>> locale: >>> > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_ CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDEN TIFICATION=C >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 >> genefilter_1.22.0 >>> [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 Biobase_2.2.2 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 >>> [4] preprocessCore_1.4.0 RSQLite_0.7-1 >>> >>> For the relase, I am new to R and Bioconductor. I have started the 12 >> May... >>> SO I think that I use the lastest. Is's the same thing with my computer >> OS. >>> My first job was to install everything. I am newly out of school for the >>> summer. >> Actually, you have an old version of R and BioC. You want to upgrade to >> R-2.9.0 and BioC 2.4 and then see if you still have the same problem >> >> Best, >> >> Jim >> >> >>> >>> >>> Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: >>> >>>> Simon No?l ha scritto: >>>>> Hello. I have some problem using qc(). I have an old data set that work >>>>> perfectly with qc() but a nuw one just arrive from affymetrix and I am >> not >>>> able >>>>> to run qc() on it. I use the code : >>>>> >>>>> library(affy) >>>>> >>>>> >>>>> >>>>> library(affyio) >>>>> >>>>> >>>>> library(simpleaffy) >>>>> >>>>> Data <-ReadAffy() >>>>> >>>>> qc <- qc(Data) >>>>> >>>>> and I recive this error message : >>>>> >>>>> *** caught segfault *** >>>>> address 0xb6cf9000, cause 'invalid permissions' >>>>> >>>>> Traceback: >>>>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, >> x]), >>>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), >>>>> as.double(st), exprs = double(length(unique.pns)), length(unique.pns), >>>>> PACKAGE = "simpleaffy") >>>>> 2: FUN(1:2[[1L]], ...) >>>>> 3: lapply(X, FUN, ...) >>>>> 4: sapply(1:length(pms[1, ]), function(x) { .C("GetExpressionLevels", >>>>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), >>>>> as.integer(length(mms[, x])), as.double(ct), as.double(st), exprs >> = >>>>> double(length(unique.pns)), length(unique.pns), PACKAGE = >>>>> "simpleaffy")$exprs}) >>>>> 5: justMAS(x, tgt = sc) >>>>> 6: call.exprs(unnormalised, "mas5") >>>>> 7: qc.affy(unnormalised, ...) >>>>> 8: qc(Data) >>>>> 9: qc(Data) >>>>> 10: eval.with.vis(expr, envir, enclos) >>>>> 11: eval.with.vis(ei, envir) >>>>> 12: source("tmp.R") >>>>> >>>>> Possible actions: >>>>> 1: abort (with core dump, if enabled) >>>>> 2: normal R exit >>>>> 3: exit R without saving workspace >>>>> 4: exit R saving workspace >>>>> Selection: >>>>> >>>>> What should I do to correct the problem? >>>>> >>>>> Simon No?l >>>>> VP Externe CADEUL >>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>>>> informatique et Microbiologie de l'Universit? Laval >>>>> CdeC >>>> >>>> Dear Simon >>>> >>>> what is your "sessionInfo()"? >>>> >>>> Are you using the latest release of R (2.9) and Bioconductor? >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> ------------------------------------------------ >>>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber >>>> >>>> >>> >>> Simon No?l >>> VP Externe CADEUL >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>> informatique et Microbiologie de l'Universit? Laval >>> CdeC >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLY •
0
Entering edit mode
I try and I recive the same result has you. The function seem to work. On an ond set of chip it work perfectly. The one I am trying to test with qc() but not working is a custum chip using hursta2a520709cdf The file just arrive from affymetrix last friday Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > Weird. What kind of chip? > > Does this work for you? > > library(simpleaffy) > library(affydata) > data(Dilution) > qc(Dilution) > > I get > > > qc(Dilution) > An object of class "QCStats" > Slot "scale.factors": > [1] 0.8934013 1.2653627 1.1448430 1.8454067 > > Slot "target": > [1] 100 > > Slot "percent.present": > 20A.present 20B.present 10A.present 10B.present > 48.79208 49.82178 49.37822 49.75842 > > Slot "average.background": > 20A 20B 10A 10B > 94.25323 63.63855 80.09436 54.25830 > > Slot "minimum.background": > 20A 20B 10A 10B > 89.52555 60.01397 77.32196 49.22574 > > Slot "maximum.background": > 20A 20B 10A 10B > 97.66280 68.18998 83.24646 57.62283 > > Slot "spikes": > AFFX-BioB-3_at AFFX-BioC-3_at AFFX-BioDn-3_at AFFX-CreX-3_at > 20A 11.64085 7.979776 11.92078 7.879601 > 20B 11.23099 7.682558 11.72899 7.752151 > 10A 11.89294 8.191754 12.20780 7.888115 > 10B 12.18343 8.644352 12.50579 8.357746 > > Slot "qc.probes": > AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at AFFX- HSAC07/X00351_M_at > 20A 12.43699 11.74085 12.30966 > 20B 12.29240 11.57156 12.11278 > 10A 12.78294 11.91173 12.57164 > 10B 12.70788 11.77651 12.43533 > AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at > 20A 12.12079 11.67781 > 20B 11.95684 11.60385 > 10A 12.26970 11.83704 > 10B 12.30909 11.73642 > AFFX-HUMGAPDH/M33197_M_at > 20A 12.18103 > 20B 11.97050 > 10A 11.84595 > 10B 12.19650 > > Slot "bioBCalls": > 20A.present 20B.present 10A.present 10B.present > "P" "P" "P" "P" > > Slot "arraytype": > [1] "hgu95av2cdf" > > > 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 datasets utils methods base > > other attached packages: > [1] hgu95av2cdf_2.4.0 affydata_1.11.5 simpleaffy_2.20.0 > gcrma_2.15.5 > [5] Biostrings_2.11.53 IRanges_1.1.66 genefilter_1.23.4 > affy_1.21.10 > [9] Biobase_2.3.11 > > loaded via a namespace (and not attached): > [1] affyio_1.11.3 annotate_1.21.5 AnnotationDbi_1.5.23 > [4] DBI_0.2-4 preprocessCore_1.5.3 RSQLite_0.7-1 > [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [10] xtable_1.5-5 > > > > Simon No?l wrote: > > Hello. I think that every thing is updated now. I still get the error. > > > > My new sessionInfo() is > > > > R version 2.9.0 (2009-04-17) > > i486-pc-linux-gnu > > > > locale: > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 > > [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 > > [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 > > [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 > > > > > > > > > > Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > > > >> Hi Simon, > >> > >> Simon No?l wrote: > >>> My sessionInfo() is > >>> > >>> R version 2.8.1 (2008-12-22) > >>> i486-pc-linux-gnu > >>> > >>> locale: > >>> > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > >>> attached base packages: > >>> [1] splines tools stats graphics grDevices utils datasets > >>> [8] methods base > >>> > >>> other attached packages: > >>> [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > >> genefilter_1.22.0 > >>> [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 > Biobase_2.2.2 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 > >>> [4] preprocessCore_1.4.0 RSQLite_0.7-1 > >>> > >>> For the relase, I am new to R and Bioconductor. I have started the 12 > >> May... > >>> SO I think that I use the lastest. Is's the same thing with my computer > >> OS. > >>> My first job was to install everything. I am newly out of school for the > >>> summer. > >> Actually, you have an old version of R and BioC. You want to upgrade to > >> R-2.9.0 and BioC 2.4 and then see if you still have the same problem > >> > >> Best, > >> > >> Jim > >> > >> > >>> > >>> > >>> Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > >>> > >>>> Simon No?l ha scritto: > >>>>> Hello. I have some problem using qc(). I have an old data set that > work > >>>>> perfectly with qc() but a nuw one just arrive from affymetrix and I am > >> not > >>>> able > >>>>> to run qc() on it. I use the code : > >>>>> > >>>>> library(affy) > >>>>> > >>>>> > >>>>> > >>>>> library(affyio) > >>>>> > >>>>> > >>>>> library(simpleaffy) > >>>>> > >>>>> Data <-ReadAffy() > >>>>> > >>>>> qc <- qc(Data) > >>>>> > >>>>> and I recive this error message : > >>>>> > >>>>> *** caught segfault *** > >>>>> address 0xb6cf9000, cause 'invalid permissions' > >>>>> > >>>>> Traceback: > >>>>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, > >> x]), > >>>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), > >>>>> as.double(st), exprs = double(length(unique.pns)), length(unique.pns), > >>>>> PACKAGE = "simpleaffy") > >>>>> 2: FUN(1:2[[1L]], ...) > >>>>> 3: lapply(X, FUN, ...) > >>>>> 4: sapply(1:length(pms[1, ]), function(x) { > .C("GetExpressionLevels", > >>>>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > >>>>> as.integer(length(mms[, x])), as.double(ct), as.double(st), > exprs > >> = > >>>>> double(length(unique.pns)), length(unique.pns), PACKAGE = > >>>>> "simpleaffy")$exprs}) > >>>>> 5: justMAS(x, tgt = sc) > >>>>> 6: call.exprs(unnormalised, "mas5") > >>>>> 7: qc.affy(unnormalised, ...) > >>>>> 8: qc(Data) > >>>>> 9: qc(Data) > >>>>> 10: eval.with.vis(expr, envir, enclos) > >>>>> 11: eval.with.vis(ei, envir) > >>>>> 12: source("tmp.R") > >>>>> > >>>>> Possible actions: > >>>>> 1: abort (with core dump, if enabled) > >>>>> 2: normal R exit > >>>>> 3: exit R without saving workspace > >>>>> 4: exit R saving workspace > >>>>> Selection: > >>>>> > >>>>> What should I do to correct the problem? > >>>>> > >>>>> Simon No?l > >>>>> VP Externe CADEUL > >>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>>>> informatique et Microbiologie de l'Universit? Laval > >>>>> CdeC > >>>> > >>>> Dear Simon > >>>> > >>>> what is your "sessionInfo()"? > >>>> > >>>> Are you using the latest release of R (2.9) and Bioconductor? > >>>> > >>>> Best wishes > >>>> Wolfgang > >>>> > >>>> ------------------------------------------------ > >>>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > >>>> > >>>> > >>> > >>> Simon No?l > >>> VP Externe CADEUL > >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>> informatique et Microbiologie de l'Universit? Laval > >>> CdeC > >>> > >>> _______________________________________________ > >>> 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 > >> Douglas Lab > >> University of Michigan > >> Department of Human Genetics > >> 5912 Buhl > >> 1241 E. Catherine St. > >> Ann Arbor MI 48109-5618 > >> 734-615-7826 > >> > >> > > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
They give me the .CDF to run their chip but they don't give the .qcdef file. I have try using the info avalible in the qc package to create my own .qcdef I think everything is perfect... But maby I have made a mistake? array hursta2a520709cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 19.05.2009: > I try and I recive the same result has you. The function seem to work. On > an > ond set of chip it work perfectly. The one I am trying to test with qc() but > not working is a custum chip using hursta2a520709cdf The file just arrive > from > affymetrix last friday > > > Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > > > Weird. What kind of chip? > > > > Does this work for you? > > > > library(simpleaffy) > > library(affydata) > > data(Dilution) > > qc(Dilution) > > > > I get > > > > > qc(Dilution) > > An object of class "QCStats" > > Slot "scale.factors": > > [1] 0.8934013 1.2653627 1.1448430 1.8454067 > > > > Slot "target": > > [1] 100 > > > > Slot "percent.present": > > 20A.present 20B.present 10A.present 10B.present > > 48.79208 49.82178 49.37822 49.75842 > > > > Slot "average.background": > > 20A 20B 10A 10B > > 94.25323 63.63855 80.09436 54.25830 > > > > Slot "minimum.background": > > 20A 20B 10A 10B > > 89.52555 60.01397 77.32196 49.22574 > > > > Slot "maximum.background": > > 20A 20B 10A 10B > > 97.66280 68.18998 83.24646 57.62283 > > > > Slot "spikes": > > AFFX-BioB-3_at AFFX-BioC-3_at AFFX-BioDn-3_at AFFX-CreX-3_at > > 20A 11.64085 7.979776 11.92078 7.879601 > > 20B 11.23099 7.682558 11.72899 7.752151 > > 10A 11.89294 8.191754 12.20780 7.888115 > > 10B 12.18343 8.644352 12.50579 8.357746 > > > > Slot "qc.probes": > > AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at > AFFX-HSAC07/X00351_M_at > > 20A 12.43699 11.74085 12.30966 > > 20B 12.29240 11.57156 12.11278 > > 10A 12.78294 11.91173 12.57164 > > 10B 12.70788 11.77651 12.43533 > > AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at > > 20A 12.12079 11.67781 > > 20B 11.95684 11.60385 > > 10A 12.26970 11.83704 > > 10B 12.30909 11.73642 > > AFFX-HUMGAPDH/M33197_M_at > > 20A 12.18103 > > 20B 11.97050 > > 10A 11.84595 > > 10B 12.19650 > > > > Slot "bioBCalls": > > 20A.present 20B.present 10A.present 10B.present > > "P" "P" "P" "P" > > > > Slot "arraytype": > > [1] "hgu95av2cdf" > > > > > 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 datasets utils methods base > > > > other attached packages: > > [1] hgu95av2cdf_2.4.0 affydata_1.11.5 simpleaffy_2.20.0 > > gcrma_2.15.5 > > [5] Biostrings_2.11.53 IRanges_1.1.66 genefilter_1.23.4 > > affy_1.21.10 > > [9] Biobase_2.3.11 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.11.3 annotate_1.21.5 AnnotationDbi_1.5.23 > > [4] DBI_0.2-4 preprocessCore_1.5.3 RSQLite_0.7-1 > > [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 > > [10] xtable_1.5-5 > > > > > > > Simon No?l wrote: > > > Hello. I think that every thing is updated now. I still get the error. > > > > > > My new sessionInfo() is > > > > > > R version 2.9.0 (2009-04-17) > > > i486-pc-linux-gnu > > > > > > locale: > > > > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > > other attached packages: > > > [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 > > > [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 > > > > > > loaded via a namespace (and not attached): > > > [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 > > > [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 > > > [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 > > > > > > > > > > > > > > > Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > > > > > >> Hi Simon, > > >> > > >> Simon No?l wrote: > > >>> My sessionInfo() is > > >>> > > >>> R version 2.8.1 (2008-12-22) > > >>> i486-pc-linux-gnu > > >>> > > >>> locale: > > >>> > > > > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > > >>> attached base packages: > > >>> [1] splines tools stats graphics grDevices utils > datasets > > >>> [8] methods base > > >>> > > >>> other attached packages: > > >>> [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > > >> genefilter_1.22.0 > > >>> [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 > > Biobase_2.2.2 > > >>> > > >>> loaded via a namespace (and not attached): > > >>> [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 > > >>> [4] preprocessCore_1.4.0 RSQLite_0.7-1 > > >>> > > >>> For the relase, I am new to R and Bioconductor. I have started the 12 > > >> May... > > >>> SO I think that I use the lastest. Is's the same thing with my > computer > > >> OS. > > >>> My first job was to install everything. I am newly out of school for > the > > >>> summer. > > >> Actually, you have an old version of R and BioC. You want to upgrade to > > >> R-2.9.0 and BioC 2.4 and then see if you still have the same problem > > >> > > >> Best, > > >> > > >> Jim > > >> > > >> > > >>> > > >>> > > >>> Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > > >>> > > >>>> Simon No?l ha scritto: > > >>>>> Hello. I have some problem using qc(). I have an old data set that > > work > > >>>>> perfectly with qc() but a nuw one just arrive from affymetrix and I > am > > >> not > > >>>> able > > >>>>> to run qc() on it. I use the code : > > >>>>> > > >>>>> library(affy) > > >>>>> > > >>>>> > > >>>>> > > >>>>> library(affyio) > > >>>>> > > >>>>> > > >>>>> library(simpleaffy) > > >>>>> > > >>>>> Data <-ReadAffy() > > >>>>> > > >>>>> qc <- qc(Data) > > >>>>> > > >>>>> and I recive this error message : > > >>>>> > > >>>>> *** caught segfault *** > > >>>>> address 0xb6cf9000, cause 'invalid permissions' > > >>>>> > > >>>>> Traceback: > > >>>>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, > > >> x]), > > >>>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), > > >>>>> as.double(st), exprs = double(length(unique.pns)), > length(unique.pns), > > >>>>> PACKAGE = "simpleaffy") > > >>>>> 2: FUN(1:2[[1L]], ...) > > >>>>> 3: lapply(X, FUN, ...) > > >>>>> 4: sapply(1:length(pms[1, ]), function(x) { > > .C("GetExpressionLevels", > > >>>>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > > >>>>> as.integer(length(mms[, x])), as.double(ct), as.double(st), > > exprs > > >> = > > >>>>> double(length(unique.pns)), length(unique.pns), PACKAGE = > > >>>>> "simpleaffy")$exprs}) > > >>>>> 5: justMAS(x, tgt = sc) > > >>>>> 6: call.exprs(unnormalised, "mas5") > > >>>>> 7: qc.affy(unnormalised, ...) > > >>>>> 8: qc(Data) > > >>>>> 9: qc(Data) > > >>>>> 10: eval.with.vis(expr, envir, enclos) > > >>>>> 11: eval.with.vis(ei, envir) > > >>>>> 12: source("tmp.R") > > >>>>> > > >>>>> Possible actions: > > >>>>> 1: abort (with core dump, if enabled) > > >>>>> 2: normal R exit > > >>>>> 3: exit R without saving workspace > > >>>>> 4: exit R saving workspace > > >>>>> Selection: > > >>>>> > > >>>>> What should I do to correct the problem? > > >>>>> > > >>>>> Simon No?l > > >>>>> VP Externe CADEUL > > >>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > >>>>> informatique et Microbiologie de l'Universit? Laval > > >>>>> CdeC > > >>>> > > >>>> Dear Simon > > >>>> > > >>>> what is your "sessionInfo()"? > > >>>> > > >>>> Are you using the latest release of R (2.9) and Bioconductor? > > >>>> > > >>>> Best wishes > > >>>> Wolfgang > > >>>> > > >>>> ------------------------------------------------ > > >>>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > > >>>> > > >>>> > > >>> > > >>> Simon No?l > > >>> VP Externe CADEUL > > >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > >>> informatique et Microbiologie de l'Universit? Laval > > >>> CdeC > > >>> > > >>> _______________________________________________ > > >>> 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 > > >> Douglas Lab > > >> University of Michigan > > >> Department of Human Genetics > > >> 5912 Buhl > > >> 1241 E. Catherine St. > > >> Ann Arbor MI 48109-5618 > > >> 734-615-7826 > > >> > > >> > > > > > > > > > Simon No?l > > > VP Externe CADEUL > > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > > informatique et Microbiologie de l'Universit? Laval > > > CdeC > > > > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > Douglas Lab > > University of Michigan > > Department of Human Genetics > > 5912 Buhl > > 1241 E. Catherine St. > > Ann Arbor MI 48109-5618 > > 734-615-7826 > > > > > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC > > _______________________________________________ > 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 > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Do all of those probesets exist in your custom chip? It looks like you just copied what was in the vignette verbatim with th exception of the array name. The idea of the qcdef file is to use the quality control probesets from your chip - if you just put some random probe names in there you won't be passing any data to the underlying C code, which is probably why you see the segfault. Simon No?l wrote: > They give me the .CDF to run their chip but they don't give the .qcdef file. I > have try using the info avalible in the qc package to create my own .qcdef > > I think everything is perfect... But maby I have made a mistake? > > array hursta2a520709cdf > alpha1 0.05 > alpha2 0.065 > spk bioB AFFX-r2-Ec-bioB-3_at > spk bioC AFFX-r2-Ec-bioC-3_at > spk bioD AFFX-r2-Ec-bioD-3_at > spk creX AFFX-r2-P1-cre-3_at > ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at > ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at > ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at > ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at > > > Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 19.05.2009: > >> I try and I recive the same result has you. The function seem to work. On >> an >> ond set of chip it work perfectly. The one I am trying to test with qc() but >> not working is a custum chip using hursta2a520709cdf The file just arrive >> from >> affymetrix last friday >> >> >> Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: >> >>> Weird. What kind of chip? >>> >>> Does this work for you? >>> >>> library(simpleaffy) >>> library(affydata) >>> data(Dilution) >>> qc(Dilution) >>> >>> I get >>> >>> > qc(Dilution) >>> An object of class "QCStats" >>> Slot "scale.factors": >>> [1] 0.8934013 1.2653627 1.1448430 1.8454067 >>> >>> Slot "target": >>> [1] 100 >>> >>> Slot "percent.present": >>> 20A.present 20B.present 10A.present 10B.present >>> 48.79208 49.82178 49.37822 49.75842 >>> >>> Slot "average.background": >>> 20A 20B 10A 10B >>> 94.25323 63.63855 80.09436 54.25830 >>> >>> Slot "minimum.background": >>> 20A 20B 10A 10B >>> 89.52555 60.01397 77.32196 49.22574 >>> >>> Slot "maximum.background": >>> 20A 20B 10A 10B >>> 97.66280 68.18998 83.24646 57.62283 >>> >>> Slot "spikes": >>> AFFX-BioB-3_at AFFX-BioC-3_at AFFX-BioDn-3_at AFFX-CreX-3_at >>> 20A 11.64085 7.979776 11.92078 7.879601 >>> 20B 11.23099 7.682558 11.72899 7.752151 >>> 10A 11.89294 8.191754 12.20780 7.888115 >>> 10B 12.18343 8.644352 12.50579 8.357746 >>> >>> Slot "qc.probes": >>> AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at >> AFFX-HSAC07/X00351_M_at >>> 20A 12.43699 11.74085 12.30966 >>> 20B 12.29240 11.57156 12.11278 >>> 10A 12.78294 11.91173 12.57164 >>> 10B 12.70788 11.77651 12.43533 >>> AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at >>> 20A 12.12079 11.67781 >>> 20B 11.95684 11.60385 >>> 10A 12.26970 11.83704 >>> 10B 12.30909 11.73642 >>> AFFX-HUMGAPDH/M33197_M_at >>> 20A 12.18103 >>> 20B 11.97050 >>> 10A 11.84595 >>> 10B 12.19650 >>> >>> Slot "bioBCalls": >>> 20A.present 20B.present 10A.present 10B.present >>> "P" "P" "P" "P" >>> >>> Slot "arraytype": >>> [1] "hgu95av2cdf" >>> >>> > 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 datasets utils methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_2.4.0 affydata_1.11.5 simpleaffy_2.20.0 >>> gcrma_2.15.5 >>> [5] Biostrings_2.11.53 IRanges_1.1.66 genefilter_1.23.4 >>> affy_1.21.10 >>> [9] Biobase_2.3.11 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.11.3 annotate_1.21.5 AnnotationDbi_1.5.23 >>> [4] DBI_0.2-4 preprocessCore_1.5.3 RSQLite_0.7-1 >>> [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 >>> [10] xtable_1.5-5 >>> > >>> >>> Simon No?l wrote: >>>> Hello. I think that every thing is updated now. I still get the error. >>>> >>>> My new sessionInfo() is >>>> >>>> R version 2.9.0 (2009-04-17) >>>> i486-pc-linux-gnu >>>> >>>> locale: >>>> > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_ CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDEN TIFICATION=C >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 >>>> [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 >>>> [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 >>>> [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 >>>> >>>> >>>> >>>> >>>> Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: >>>> >>>>> Hi Simon, >>>>> >>>>> Simon No?l wrote: >>>>>> My sessionInfo() is >>>>>> >>>>>> R version 2.8.1 (2008-12-22) >>>>>> i486-pc-linux-gnu >>>>>> >>>>>> locale: >>>>>> > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_ CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDEN TIFICATION=C >>>>>> attached base packages: >>>>>> [1] splines tools stats graphics grDevices utils >> datasets >>>>>> [8] methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 >>>>> genefilter_1.22.0 >>>>>> [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 >>> Biobase_2.2.2 >>>>>> loaded via a namespace (and not attached): >>>>>> [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 >>>>>> [4] preprocessCore_1.4.0 RSQLite_0.7-1 >>>>>> >>>>>> For the relase, I am new to R and Bioconductor. I have started the 12 >>>>> May... >>>>>> SO I think that I use the lastest. Is's the same thing with my >> computer >>>>> OS. >>>>>> My first job was to install everything. I am newly out of school for >> the >>>>>> summer. >>>>> Actually, you have an old version of R and BioC. You want to upgrade to >>>>> R-2.9.0 and BioC 2.4 and then see if you still have the same problem >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>>> >>>>>> Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: >>>>>> >>>>>>> Simon No?l ha scritto: >>>>>>>> Hello. I have some problem using qc(). I have an old data set that >>> work >>>>>>>> perfectly with qc() but a nuw one just arrive from affymetrix and I >> am >>>>> not >>>>>>> able >>>>>>>> to run qc() on it. I use the code : >>>>>>>> >>>>>>>> library(affy) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> library(affyio) >>>>>>>> >>>>>>>> >>>>>>>> library(simpleaffy) >>>>>>>> >>>>>>>> Data <-ReadAffy() >>>>>>>> >>>>>>>> qc <- qc(Data) >>>>>>>> >>>>>>>> and I recive this error message : >>>>>>>> >>>>>>>> *** caught segfault *** >>>>>>>> address 0xb6cf9000, cause 'invalid permissions' >>>>>>>> >>>>>>>> Traceback: >>>>>>>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, >>>>> x]), >>>>>>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), >>>>>>>> as.double(st), exprs = double(length(unique.pns)), >> length(unique.pns), >>>>>>>> PACKAGE = "simpleaffy") >>>>>>>> 2: FUN(1:2[[1L]], ...) >>>>>>>> 3: lapply(X, FUN, ...) >>>>>>>> 4: sapply(1:length(pms[1, ]), function(x) { >>> .C("GetExpressionLevels", >>>>>>>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), >>>>>>>> as.integer(length(mms[, x])), as.double(ct), as.double(st), >>> exprs >>>>> = >>>>>>>> double(length(unique.pns)), length(unique.pns), PACKAGE = >>>>>>>> "simpleaffy")$exprs}) >>>>>>>> 5: justMAS(x, tgt = sc) >>>>>>>> 6: call.exprs(unnormalised, "mas5") >>>>>>>> 7: qc.affy(unnormalised, ...) >>>>>>>> 8: qc(Data) >>>>>>>> 9: qc(Data) >>>>>>>> 10: eval.with.vis(expr, envir, enclos) >>>>>>>> 11: eval.with.vis(ei, envir) >>>>>>>> 12: source("tmp.R") >>>>>>>> >>>>>>>> Possible actions: >>>>>>>> 1: abort (with core dump, if enabled) >>>>>>>> 2: normal R exit >>>>>>>> 3: exit R without saving workspace >>>>>>>> 4: exit R saving workspace >>>>>>>> Selection: >>>>>>>> >>>>>>>> What should I do to correct the problem? >>>>>>>> >>>>>>>> Simon No?l >>>>>>>> VP Externe CADEUL >>>>>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>>>>>>> informatique et Microbiologie de l'Universit? Laval >>>>>>>> CdeC >>>>>>> Dear Simon >>>>>>> >>>>>>> what is your "sessionInfo()"? >>>>>>> >>>>>>> Are you using the latest release of R (2.9) and Bioconductor? >>>>>>> >>>>>>> Best wishes >>>>>>> Wolfgang >>>>>>> >>>>>>> ------------------------------------------------ >>>>>>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber >>>>>>> >>>>>>> >>>>>> Simon No?l >>>>>> VP Externe CADEUL >>>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>>>>> informatique et Microbiologie de l'Universit? Laval >>>>>> CdeC >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> >>>>> >>>> >>>> Simon No?l >>>> VP Externe CADEUL >>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >>>> informatique et Microbiologie de l'Universit? Laval >>>> CdeC >>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> >>> >> >> Simon No?l >> VP Externe CADEUL >> Association des ?tudiants et ?tudiantes en Biochimie, Bio- >> informatique et Microbiologie de l'Universit? Laval >> CdeC >> >> _______________________________________________ >> 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 >> >> > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLY •
0
Entering edit mode
I do the research before to be sure that the probeset indicated were in my chip and they are. A also verify the name to be sure that the capital letter are the same. I also look at other .qcdef files to see how they were made and with those information, a made my .qcdef file and a second .qcdef file for my chip, again veryfing correctly the name of the probe and their presence on the chip, i tried my second .qcdef file. I got the same error. My second .qcdef is array hursta2a520709cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-BioB-3_at spk bioC AFFX-BioC-3_at spk bioD AFFX-BioDn-3_at spk creX AFFX-CreX-3_at ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at For the last four line, I didn't change anything. In every human .qcdef that I have, they were the same. Again, I am sure that these probeset are on my chip and the capital letter are the same. Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > Do all of those probesets exist in your custom chip? It looks like you > just copied what was in the vignette verbatim with th exception of the > array name. > > The idea of the qcdef file is to use the quality control probesets from > your chip - if you just put some random probe names in there you won't > be passing any data to the underlying C code, which is probably why you > see the segfault. > > Simon No?l wrote: > > They give me the .CDF to run their chip but they don't give the .qcdef > file. I > > have try using the info avalible in the qc package to create my own .qcdef > > > > I think everything is perfect... But maby I have made a mistake? > > > > array hursta2a520709cdf > > alpha1 0.05 > > alpha2 0.065 > > spk bioB AFFX-r2-Ec-bioB-3_at > > spk bioC AFFX-r2-Ec-bioC-3_at > > spk bioD AFFX-r2-Ec-bioD-3_at > > spk creX AFFX-r2-P1-cre-3_at > > ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX- HSAC07/X00351_5_at > > ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX- HSAC07/X00351_M_at > > ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at > > ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at > > > > > > Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 19.05.2009: > > > >> I try and I recive the same result has you. The function seem to work. > On > >> an > >> ond set of chip it work perfectly. The one I am trying to test with qc() > but > >> not working is a custum chip using hursta2a520709cdf The file just arrive > >> from > >> affymetrix last friday > >> > >> > >> Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > >> > >>> Weird. What kind of chip? > >>> > >>> Does this work for you? > >>> > >>> library(simpleaffy) > >>> library(affydata) > >>> data(Dilution) > >>> qc(Dilution) > >>> > >>> I get > >>> > >>> > qc(Dilution) > >>> An object of class "QCStats" > >>> Slot "scale.factors": > >>> [1] 0.8934013 1.2653627 1.1448430 1.8454067 > >>> > >>> Slot "target": > >>> [1] 100 > >>> > >>> Slot "percent.present": > >>> 20A.present 20B.present 10A.present 10B.present > >>> 48.79208 49.82178 49.37822 49.75842 > >>> > >>> Slot "average.background": > >>> 20A 20B 10A 10B > >>> 94.25323 63.63855 80.09436 54.25830 > >>> > >>> Slot "minimum.background": > >>> 20A 20B 10A 10B > >>> 89.52555 60.01397 77.32196 49.22574 > >>> > >>> Slot "maximum.background": > >>> 20A 20B 10A 10B > >>> 97.66280 68.18998 83.24646 57.62283 > >>> > >>> Slot "spikes": > >>> AFFX-BioB-3_at AFFX-BioC-3_at AFFX-BioDn-3_at AFFX-CreX- 3_at > >>> 20A 11.64085 7.979776 11.92078 7.879601 > >>> 20B 11.23099 7.682558 11.72899 7.752151 > >>> 10A 11.89294 8.191754 12.20780 7.888115 > >>> 10B 12.18343 8.644352 12.50579 8.357746 > >>> > >>> Slot "qc.probes": > >>> AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at > >> AFFX-HSAC07/X00351_M_at > >>> 20A 12.43699 11.74085 > 12.30966 > >>> 20B 12.29240 11.57156 > 12.11278 > >>> 10A 12.78294 11.91173 > 12.57164 > >>> 10B 12.70788 11.77651 > 12.43533 > >>> AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at > >>> 20A 12.12079 11.67781 > >>> 20B 11.95684 11.60385 > >>> 10A 12.26970 11.83704 > >>> 10B 12.30909 11.73642 > >>> AFFX-HUMGAPDH/M33197_M_at > >>> 20A 12.18103 > >>> 20B 11.97050 > >>> 10A 11.84595 > >>> 10B 12.19650 > >>> > >>> Slot "bioBCalls": > >>> 20A.present 20B.present 10A.present 10B.present > >>> "P" "P" "P" "P" > >>> > >>> Slot "arraytype": > >>> [1] "hgu95av2cdf" > >>> > >>> > 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 datasets utils methods base > >>> > >>> other attached packages: > >>> [1] hgu95av2cdf_2.4.0 affydata_1.11.5 simpleaffy_2.20.0 > >>> gcrma_2.15.5 > >>> [5] Biostrings_2.11.53 IRanges_1.1.66 genefilter_1.23.4 > >>> affy_1.21.10 > >>> [9] Biobase_2.3.11 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] affyio_1.11.3 annotate_1.21.5 AnnotationDbi_1.5.23 > >>> [4] DBI_0.2-4 preprocessCore_1.5.3 RSQLite_0.7-1 > >>> [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 > >>> [10] xtable_1.5-5 > >>> > > >>> > >>> Simon No?l wrote: > >>>> Hello. I think that every thing is updated now. I still get the error. > >>>> > >>>> My new sessionInfo() is > >>>> > >>>> R version 2.9.0 (2009-04-17) > >>>> i486-pc-linux-gnu > >>>> > >>>> locale: > >>>> > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > >>>> attached base packages: > >>>> [1] stats graphics grDevices utils datasets methods base > >>>> > >>>> other attached packages: > >>>> [1] simpleaffy_2.20.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.2 > >>>> [5] genefilter_1.24.0 affyio_1.12.0 affy_1.22.0 Biobase_2.4.1 > >>>> > >>>> loaded via a namespace (and not attached): > >>>> [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 > >>>> [4] preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 > >>>> [7] survival_2.35-4 tools_2.9.0 xtable_1.5-5 > >>>> > >>>> > >>>> > >>>> > >>>> Selon "James W. MacDonald" <jmacdon at="" med.umich.edu="">, 19.05.2009: > >>>> > >>>>> Hi Simon, > >>>>> > >>>>> Simon No?l wrote: > >>>>>> My sessionInfo() is > >>>>>> > >>>>>> R version 2.8.1 (2008-12-22) > >>>>>> i486-pc-linux-gnu > >>>>>> > >>>>>> locale: > >>>>>> > > > LC_CTYPE=fr_CA.UTF-8;LC_NUMERIC=C;LC_TIME=fr_CA.UTF-8;LC_COLLATE=fr_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_CA.UTF-8;LC_PAPER=fr_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_CA.UTF-8;LC_IDENTI FICATION=C > >>>>>> attached base packages: > >>>>>> [1] splines tools stats graphics grDevices utils > >> datasets > >>>>>> [8] methods base > >>>>>> > >>>>>> other attached packages: > >>>>>> [1] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > >>>>> genefilter_1.22.0 > >>>>>> [5] survival_2.35-4 affyio_1.10.1 affy_1.20.2 > >>> Biobase_2.2.2 > >>>>>> loaded via a namespace (and not attached): > >>>>>> [1] annotate_1.20.1 AnnotationDbi_1.4.3 DBI_0.2-4 > >>>>>> [4] preprocessCore_1.4.0 RSQLite_0.7-1 > >>>>>> > >>>>>> For the relase, I am new to R and Bioconductor. I have started the 12 > >>>>> May... > >>>>>> SO I think that I use the lastest. Is's the same thing with my > >> computer > >>>>> OS. > >>>>>> My first job was to install everything. I am newly out of school for > >> the > >>>>>> summer. > >>>>> Actually, you have an old version of R and BioC. You want to upgrade to > >>>>> R-2.9.0 and BioC 2.4 and then see if you still have the same problem > >>>>> > >>>>> Best, > >>>>> > >>>>> Jim > >>>>> > >>>>> > >>>>>> > >>>>>> Selon Wolfgang Huber <huber at="" ebi.ac.uk="">, 17.05.2009: > >>>>>> > >>>>>>> Simon No?l ha scritto: > >>>>>>>> Hello. I have some problem using qc(). I have an old data set that > >>> work > >>>>>>>> perfectly with qc() but a nuw one just arrive from affymetrix and I > >> am > >>>>> not > >>>>>>> able > >>>>>>>> to run qc() on it. I use the code : > >>>>>>>> > >>>>>>>> library(affy) > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> library(affyio) > >>>>>>>> > >>>>>>>> > >>>>>>>> library(simpleaffy) > >>>>>>>> > >>>>>>>> Data <-ReadAffy() > >>>>>>>> > >>>>>>>> qc <- qc(Data) > >>>>>>>> > >>>>>>>> and I recive this error message : > >>>>>>>> > >>>>>>>> *** caught segfault *** > >>>>>>>> address 0xb6cf9000, cause 'invalid permissions' > >>>>>>>> > >>>>>>>> Traceback: > >>>>>>>> 1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[, > >>>>> x]), > >>>>>>>> as.character(pns), as.integer(length(mms[, x])), as.double(ct), > >>>>>>>> as.double(st), exprs = double(length(unique.pns)), > >> length(unique.pns), > >>>>>>>> PACKAGE = "simpleaffy") > >>>>>>>> 2: FUN(1:2[[1L]], ...) > >>>>>>>> 3: lapply(X, FUN, ...) > >>>>>>>> 4: sapply(1:length(pms[1, ]), function(x) { > >>> .C("GetExpressionLevels", > >>>>>>>> as.double(pms[, x]), as.double(mms[, x]), as.character(pns), > >>>>>>>> as.integer(length(mms[, x])), as.double(ct), as.double(st), > >>> exprs > >>>>> = > >>>>>>>> double(length(unique.pns)), length(unique.pns), PACKAGE = > >>>>>>>> "simpleaffy")$exprs}) > >>>>>>>> 5: justMAS(x, tgt = sc) > >>>>>>>> 6: call.exprs(unnormalised, "mas5") > >>>>>>>> 7: qc.affy(unnormalised, ...) > >>>>>>>> 8: qc(Data) > >>>>>>>> 9: qc(Data) > >>>>>>>> 10: eval.with.vis(expr, envir, enclos) > >>>>>>>> 11: eval.with.vis(ei, envir) > >>>>>>>> 12: source("tmp.R") > >>>>>>>> > >>>>>>>> Possible actions: > >>>>>>>> 1: abort (with core dump, if enabled) > >>>>>>>> 2: normal R exit > >>>>>>>> 3: exit R without saving workspace > >>>>>>>> 4: exit R saving workspace > >>>>>>>> Selection: > >>>>>>>> > >>>>>>>> What should I do to correct the problem? > >>>>>>>> > >>>>>>>> Simon No?l > >>>>>>>> VP Externe CADEUL > >>>>>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>>>>>>> informatique et Microbiologie de l'Universit? Laval > >>>>>>>> CdeC > >>>>>>> Dear Simon > >>>>>>> > >>>>>>> what is your "sessionInfo()"? > >>>>>>> > >>>>>>> Are you using the latest release of R (2.9) and Bioconductor? > >>>>>>> > >>>>>>> Best wishes > >>>>>>> Wolfgang > >>>>>>> > >>>>>>> ------------------------------------------------ > >>>>>>> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > >>>>>>> > >>>>>>> > >>>>>> Simon No?l > >>>>>> VP Externe CADEUL > >>>>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>>>>> informatique et Microbiologie de l'Universit? Laval > >>>>>> CdeC > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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 > >>>>> Douglas Lab > >>>>> University of Michigan > >>>>> Department of Human Genetics > >>>>> 5912 Buhl > >>>>> 1241 E. Catherine St. > >>>>> Ann Arbor MI 48109-5618 > >>>>> 734-615-7826 > >>>>> > >>>>> > >>>> > >>>> Simon No?l > >>>> VP Externe CADEUL > >>>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>>> informatique et Microbiologie de l'Universit? Laval > >>>> CdeC > >>>> > >>> -- > >>> James W. MacDonald, M.S. > >>> Biostatistician > >>> Douglas Lab > >>> University of Michigan > >>> Department of Human Genetics > >>> 5912 Buhl > >>> 1241 E. Catherine St. > >>> Ann Arbor MI 48109-5618 > >>> 734-615-7826 > >>> > >>> > >> > >> Simon No?l > >> VP Externe CADEUL > >> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >> informatique et Microbiologie de l'Universit? Laval > >> CdeC > >> > >> _______________________________________________ > >> 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 > >> > >> > > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Hello every one. I have a question. I have a gene list in a .xls like probeID Symbol 1030431 ACSL1 4610431 ACTG2 4810575 ADAMTSL2 1510750 ADH1C 4060519 ADORA1 5720523 ADRA2A 2810482 AHNAK 1260270 AIM2 4180768 ALAS2 ... ... I want to plote all of those genes on their chromosome. How can I do this? Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Hi Simon, Not a good idea to start a new thread by replying to a different thread you started previously. Then it shows up under the previous thread even if you changed the subject. more below... Simon No?l wrote: > Hello every one. I have a question. I have a gene list in a .xls like > > probeID Symbol > 1030431 ACSL1 > 4610431 ACTG2 > 4810575 ADAMTSL2 > 1510750 ADH1C > 4060519 ADORA1 > 5720523 ADRA2A > 2810482 AHNAK > 1260270 AIM2 > 4180768 ALAS2 > ... ... > > I want to plote all of those genes on their chromosome. How can I do this? So first you need to map each gene to its chromosome location. You can use one of the org.*.eg.db annotation packages for this (pick up the one for your organism): http://bioconductor.org/packages/release/data/annotation/ and use the SYMBOL2EG map to map your gene symbols to their corresponding Entrez IDs and then the CHRLOC map to map your Entrez IDs to their chromosome locations. Example: library(org.Hs.eg.db) mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C", "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2") myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG)) mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC))) One thing to be aware of is that those mappings are not necessarily one-to-one e.g. the same symbol can be associated with different genes: > flat <- toTable(org.Hs.egSYMBOL2EG) > names(flat) [1] "gene_id" "symbol" > any(duplicated(flat$gene_id)) [1] FALSE > any(duplicated(flat$symbol)) [1] TRUE The same thing happens with the org.Hs.egCHRLOC map (I'm not sure why we have this though, may be others on the list can explain). Anyway this explains why 'mylocs' can have more elements than 'mysymbols'. Cheers, H. > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLY •
0
Entering edit mode
I am sorry. Has I say, I am new to R and bioconductor. I am still learning. I will try this tomorow and I will write you back to tell you the result. Thank's you for your help. Il it's working, I will only have to wory about my problem with qc()... Or at least for now. The summer is really young;) Selon Hervé Pagès <hpages at="" fhcrc.org="">, 21.05.2009: > Hi Simon, > > Not a good idea to start a new thread by replying to a different thread > you started previously. Then it shows up under the previous thread even > if you changed the subject. > > more below... > > Simon No?l wrote: > > Hello every one. I have a question. I have a gene list in a .xls like > > > > probeID Symbol > > 1030431 ACSL1 > > 4610431 ACTG2 > > 4810575 ADAMTSL2 > > 1510750 ADH1C > > 4060519 ADORA1 > > 5720523 ADRA2A > > 2810482 AHNAK > > 1260270 AIM2 > > 4180768 ALAS2 > > ... ... > > > > I want to plote all of those genes on their chromosome. How can I do this? > > So first you need to map each gene to its chromosome location. > > You can use one of the org.*.eg.db annotation packages for > this (pick up the one for your organism): > > http://bioconductor.org/packages/release/data/annotation/ > > and use the SYMBOL2EG map to map your gene symbols to their corresponding > Entrez IDs and then the CHRLOC map to map your Entrez IDs to their chromosome > locations. > > Example: > > library(org.Hs.eg.db) > mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C", > "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2") > myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG)) > mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC))) > > One thing to be aware of is that those mappings are not necessarily > one-to-one e.g. the same symbol can be associated with different genes: > > > flat <- toTable(org.Hs.egSYMBOL2EG) > > names(flat) > [1] "gene_id" "symbol" > > any(duplicated(flat$gene_id)) > [1] FALSE > > any(duplicated(flat$symbol)) > [1] TRUE > > The same thing happens with the org.Hs.egCHRLOC map (I'm not sure > why we have this though, may be others on the list can explain). > > Anyway this explains why 'mylocs' can have more elements than 'mysymbols'. > > Cheers, > H. > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > _______________________________________________ > > 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 > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
I have try your procedure and every thing is loking fine for now. What's the netx step to plot my genes on their chromosomes? Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 21.05.2009: > I am sorry. Has I say, I am new to R and bioconductor. I am still learning. > > I will try this tomorow and I will write you back to tell you the result. > Thank's you for your help. Il it's working, I will only have to wory about > my > problem with qc()... Or at least for now. The summer is really young;) > Selon Hervé Pagès <hpages at="" fhcrc.org="">, 21.05.2009: > > > Hi Simon, > > > > Not a good idea to start a new thread by replying to a different thread > > you started previously. Then it shows up under the previous thread even > > if you changed the subject. > > > > more below... > > > > Simon No?l wrote: > > > Hello every one. I have a question. I have a gene list in a .xls like > > > > > > probeID Symbol > > > 1030431 ACSL1 > > > 4610431 ACTG2 > > > 4810575 ADAMTSL2 > > > 1510750 ADH1C > > > 4060519 ADORA1 > > > 5720523 ADRA2A > > > 2810482 AHNAK > > > 1260270 AIM2 > > > 4180768 ALAS2 > > > ... ... > > > > > > I want to plote all of those genes on their chromosome. How can I do > this? > > > > So first you need to map each gene to its chromosome location. > > > > You can use one of the org.*.eg.db annotation packages for > > this (pick up the one for your organism): > > > > http://bioconductor.org/packages/release/data/annotation/ > > > > and use the SYMBOL2EG map to map your gene symbols to their corresponding > > Entrez IDs and then the CHRLOC map to map your Entrez IDs to their > chromosome > > locations. > > > > Example: > > > > library(org.Hs.eg.db) > > mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C", > > "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2") > > myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG)) > > mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC))) > > > > One thing to be aware of is that those mappings are not necessarily > > one-to-one e.g. the same symbol can be associated with different genes: > > > > > flat <- toTable(org.Hs.egSYMBOL2EG) > > > names(flat) > > [1] "gene_id" "symbol" > > > any(duplicated(flat$gene_id)) > > [1] FALSE > > > any(duplicated(flat$symbol)) > > [1] TRUE > > > > The same thing happens with the org.Hs.egCHRLOC map (I'm not sure > > why we have this though, may be others on the list can explain). > > > > Anyway this explains why 'mylocs' can have more elements than 'mysymbols'. > > > > Cheers, > > H. > > > > > > > > Simon No?l > > > VP Externe CADEUL > > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > > informatique et Microbiologie de l'Universit? Laval > > > CdeC > > > > > > _______________________________________________ > > > 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 > > > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N, M2-B876 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpages at fhcrc.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > > > > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •
0
Entering edit mode
Whell, now I got the result I wanted. In R, I use >library(org.Hs.eg.db) >mysymbols <- scan("./Gene_list.csv", what = 'character', skip =1) >myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG)) >write.table(myEgIDs,file="myEgIDs.xls") After, I use my .xls with the program stripe. Thans's you for your help. Does anyone have an idea about my problem with qc()? Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 23.05.2009: > I have try your procedure and every thing is loking fine for now. What's the > netx step to plot my genes on their chromosomes? > > Selon Simon No?l <simon.noel.2 at="" ulaval.ca="">, 21.05.2009: > > > I am sorry. Has I say, I am new to R and bioconductor. I am still > learning. > > > > I will try this tomorow and I will write you back to tell you the result. > > Thank's you for your help. Il it's working, I will only have to wory about > > my > > problem with qc()... Or at least for now. The summer is really young;) > > Selon Hervé Pagès <hpages at="" fhcrc.org="">, 21.05.2009: > > > > > Hi Simon, > > > > > > Not a good idea to start a new thread by replying to a different thread > > > you started previously. Then it shows up under the previous thread even > > > if you changed the subject. > > > > > > more below... > > > > > > Simon No?l wrote: > > > > Hello every one. I have a question. I have a gene list in a .xls like > > > > > > > > probeID Symbol > > > > 1030431 ACSL1 > > > > 4610431 ACTG2 > > > > 4810575 ADAMTSL2 > > > > 1510750 ADH1C > > > > 4060519 ADORA1 > > > > 5720523 ADRA2A > > > > 2810482 AHNAK > > > > 1260270 AIM2 > > > > 4180768 ALAS2 > > > > ... ... > > > > > > > > I want to plote all of those genes on their chromosome. How can I do > > this? > > > > > > So first you need to map each gene to its chromosome location. > > > > > > You can use one of the org.*.eg.db annotation packages for > > > this (pick up the one for your organism): > > > > > > http://bioconductor.org/packages/release/data/annotation/ > > > > > > and use the SYMBOL2EG map to map your gene symbols to their corresponding > > > Entrez IDs and then the CHRLOC map to map your Entrez IDs to their > > chromosome > > > locations. > > > > > > Example: > > > > > > library(org.Hs.eg.db) > > > mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C", > > > "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2") > > > myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG)) > > > mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC))) > > > > > > One thing to be aware of is that those mappings are not necessarily > > > one-to-one e.g. the same symbol can be associated with different genes: > > > > > > > flat <- toTable(org.Hs.egSYMBOL2EG) > > > > names(flat) > > > [1] "gene_id" "symbol" > > > > any(duplicated(flat$gene_id)) > > > [1] FALSE > > > > any(duplicated(flat$symbol)) > > > [1] TRUE > > > > > > The same thing happens with the org.Hs.egCHRLOC map (I'm not sure > > > why we have this though, may be others on the list can explain). > > > > > > Anyway this explains why 'mylocs' can have more elements than > 'mysymbols'. > > > > > > Cheers, > > > H. > > > > > > > > > > > Simon No?l > > > > VP Externe CADEUL > > > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > > > informatique et Microbiologie de l'Universit? Laval > > > > CdeC > > > > > > > > _______________________________________________ > > > > 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 > > > > > > -- > > > Hervé Pagès > > > > > > Program in Computational Biology > > > Division of Public Health Sciences > > > Fred Hutchinson Cancer Research Center > > > 1100 Fairview Ave. N, M2-B876 > > > P.O. Box 19024 > > > Seattle, WA 98109-1024 > > > > > > E-mail: hpages at fhcrc.org > > > Phone: (206) 667-5791 > > > Fax: (206) 667-1319 > > > > > > > > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > Simon No?l > VP Externe CADEUL > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > informatique et Microbiologie de l'Universit? Laval > CdeC Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1038 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6