[BioC] memory invalid permission with qc()
James W. MacDonald
jmacdon at med.umich.edu
Tue May 19 17:24:39 CEST 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
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>>> 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
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