[BioC] memory invalid permission with qc()
Simon Noël
simon.noel.2 at ulaval.ca
Tue May 19 17:34:02 CEST 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
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