[BioC] memory invalid permission with qc()
Simon Noël
simon.noel.2 at ulaval.ca
Tue May 19 18:04:34 CEST 2009
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 Noël <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 Noël 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_IDENTIFICATION=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 Noël 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_IDENTIFICATION=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 Noël 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 Noël
> > >>>>> VP Externe CADEUL
> > >>>>> Association des étudiants et étudiantes en Biochimie, Bio-
> > >>>>> informatique et Microbiologie de l'Université 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 Noël
> > >>> VP Externe CADEUL
> > >>> Association des étudiants et étudiantes en Biochimie, Bio-
> > >>> informatique et Microbiologie de l'Université 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 Noël
> > > VP Externe CADEUL
> > > Association des étudiants et étudiantes en Biochimie, Bio-
> > > informatique et Microbiologie de l'Université 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 Noël
> VP Externe CADEUL
> Association des étudiants et étudiantes en Biochimie, Bio-
> informatique et Microbiologie de l'Université 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 Noël
VP Externe CADEUL
Association des étudiants et étudiantes en Biochimie, Bio-
informatique et Microbiologie de l'Université Laval
CdeC
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