[BioC] memory invalid permission with qc()
James W. MacDonald
jmacdon at med.umich.edu
Tue May 19 18:22:37 CEST 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
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