[BioC] memory invalid permission with qc()
Simon Noël
simon.noel.2 at ulaval.ca
Tue May 19 19:24:20 CEST 2009
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 Noël 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 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
> >
>
> --
> 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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