[BioC] Quality control;Missing value;installation
Mark Cowley
m.cowley at garvan.org.au
Wed Aug 13 08:01:10 CEST 2008
Yisong,
please search the archives, and post back if you still have problems:
http://search.gmane.org/?query=qcdef
cheers,
Mark
On 13/08/2008, at 1:49 PM, Yisong Zhen wrote:
> Hi,
>
> I updated my R version and Bioconductor. But I met different error,
> where
> and how to set up ".qcdef" file?
>
> library(affy)
> Tucson_data <- ReadAffy()
>
> library(affyQCReport); # Loads "affy" and "simpleaffy" packages
> QCReport(Tucson_data, file="ExampleQC.pdf")
>
> setQCEnvironment(cdfn) :
> Could not find array definition file ' cint06a520380fcdf.qcdef '.
> Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC
> parameters
> manually.
>
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE
> =
> zh_CN
> .GB18030
> ;LC_NUMERIC
> =
> C
> ;LC_TIME
> =
> zh_CN
> .GB18030
> ;LC_COLLATE
> =
> zh_CN
> .GB18030
> ;LC_MONETARY
> =
> C
> ;LC_MESSAGES
> =
> zh_CN
> .GB18030
> ;LC_PAPER
> =
> zh_CN
> .GB18030
> ;LC_NAME
> =
> C
> ;LC_ADDRESS
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils
> datasets
> [8] methods base
>
> other attached packages:
> [1] cint06a520380fcdf_1.18.0 affyQCReport_1.18.0
> geneplotter_1.18.0
> [4] annotate_1.18.0 AnnotationDbi_1.2.2
> RSQLite_0.6-9
> [7] DBI_0.2-4 lattice_0.17-8
> RColorBrewer_1.0-2
> [10] affyPLM_1.16.0 xtable_1.5-2
> simpleaffy_2.16.0
> [13] gcrma_2.12.1 matchprobes_1.12.0
> genefilter_1.20.0
> [16] survival_2.34-1 affy_1.18.2
> preprocessCore_1.2.1
> [19] affyio_1.8.1 Biobase_2.0.1
>
> loaded via a namespace (and not attached):
> [1] grid_2.7.1 KernSmooth_2.22-22
>
> I used same protocol to install the CDF file as before
>
> library(makecdfenv);
>
> make.cdf.package("CINT06a520380F.cdf ", species =
> "Ciona_intestinalis");
> R CMD INSTALL cint06a520380fcdf
>
> I read the previous messages and they have similiar question but I
> still do
> not undstand why and how to proceed?? How to set the PATH variable?
>
> Thanks in advance.
>
> Yisong
>
>
>
>
> On 8/12/08, Robert Gentleman <rgentlem at fhcrc.org> wrote:
>>
>> Hi Yisong,
>> Your R is very out of date, and we don't fix problems that are that
>> far
>> back. Please update to R 2.7.1 (preferably patched) and try again,
>> and then
>> you will be able to get arrayQualityMetrics
>>
>> best wishes
>> Robert
>>
>>
>> Yisong Zhen wrote:
>>
>>> Dear Bioconductors and Robert,
>>>
>>> This is the output,
>>>
>>> (1)
>>>
>>>> Tucson_Array
>>>>
>>> AffyBatch object
>>> size of arrays=716x716 features (8 kb)
>>> cdf=CINT06a520380F (30969 affyids)
>>> number of samples=5
>>> number of genes=30969
>>> annotation=cint06a520380f
>>> notes=
>>>
>>> (2)
>>>
>>> sessionInfo()
>>>>
>>> R version 2.5.0 (2007-04-23)
>>> i686-redhat-linux-gnu
>>>
>>> locale:
>>>
>>> LC_CTYPE
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_NUMERIC
>>> =
>>> C
>>> ;LC_TIME
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_COLLATE
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_MONETARY
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_MESSAGES
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_PAPER
>>> =
>>> zh_CN
>>> .GB18030
>>> ;LC_NAME
>>> =
>>> C
>>> ;LC_ADDRESS
>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] "tools" "stats" "graphics" "grDevices" "utils"
>>> "datasets"
>>> [7] "methods" "base"
>>>
>>> other attached packages:
>>> affy affyio Biobase
>>> "1.14.2" "1.4.1" "1.14.1"
>>> (3)
>>> When I try to install the arrayQualityMetrics, there is warning
>>> message. I
>>> cannot load the library arrayQualityMetrics.
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite("arrayQualityMetrics")
>>>>
>>> Running biocinstall version 2.0.8 with R version 2.5.0
>>> Your version of R requires version 2.0 of Bioconductor.
>>> Warning message:
>>> package 'arrayQualityMetrics' is not available in:
>>> install.packages(pkgs =
>>> pkgs, repos = repos, dependencies = dependencies,
>>>
>>>
>>> Thanks.
>>>
>>> Yisong
>>>
>>>
>>> On 8/12/08, Robert Gentleman <rgentlem at fhcrc.org> wrote:
>>>
>>>> Hi Yisong,
>>>>
>>>> Yisong Zhen wrote:
>>>>
>>>> Dear Bioconductors,
>>>>>
>>>>> I tried to get the quality control report generated by
>>>>> affyQCReport. But
>>>>> I
>>>>> failed.
>>>>>
>>>>> This is my code:
>>>>>
>>>>> library(affy);
>>>>>
>>>>> Tucson_Array <-ReadAffy();
>>>>>
>>>>> There is no need to have ; at the end of lines in R.
>>>>
>>>> Could you please post the output of sessionInfo(), as asked in the
>>>> posting
>>>> guide. Then try just
>>>>
>>>> Tucson_Array
>>>>
>>>> and let us know what happens.
>>>>
>>>> And finally, let me suggest that you try the arrayQualityMetrics
>>>> package
>>>> instead of using affyQCReport. The report it generates is a bit
>>>> more
>>>> comprehensive, but currently only in HTML (I think that will change
>>>> soon).
>>>>
>>>> best wishes
>>>> Robert
>>>>
>>>>
>>>> library(affyQCReport);
>>>>> QCReport(Tucson_Array, file="TucsonQC.pdf");
>>>>>
>>>>> This is the error message:
>>>>>
>>>>> error density.default(newX[, i], ...) :
>>>>> 'x' contains missing values
>>>>> Warning message:
>>>>> duplicate row.names
>>>>>
>>>>>
>>>>>
>>>>> 12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,54,55,59,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96,97,100,101,102,106,107,108,110,111,112,114,116,117,118,119,120,121,122,125,127,131,132,135,136,139,142,143,144,146,147,148,149,151,152,154,156,158,159,160,161,162,165,167,168,171,172,173,179,180,181,182,183,184,187,190,191,196,197,198,199,205,206,207,208,211,213,217,218,219,221,222,224,227,228,230,232,234,237,238,241,242,246,249,252,253,254,255,257,259,260,263,264,266,267,269,270,271,273,275,276,279,281,283,285,288,292,294,296,298,301,304,307,309,310,312,315,316,317,321,324,326,329,332,333,334,336,339,341,343,345,346,348,351,352,353,354,357,358,360,367,369,370,372,373,375,376,378,381,383,384,385,386,388,389,391,392,394,395,397,400,403,404,405,407,410,412,415,419,421,424,426,427,429,430,432,434,436,437,439,441,443,446,449,452,454,456,457,458,461,465,468,470,471,472,474,475,477,480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,513,5
>>>>> [... truncated] in: data.row.names(row.names, rowsi, i)
>>>>>
>>>>> How can I do for next step to deal with the missing value and
>>>>> duplicated
>>>>> row.names? And what other packages (or steps) should I select to
>>>>> assess
>>>>> the
>>>>> within-group variation so I can discard the poor quality array
>>>>> (outlying
>>>>> chips)?
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Yisong
>>>>>
>>>>>
>>>>>
>>>>> PS.
>>>>>
>>>>> And here is,
>>>>>
>>>>> sessionInfo()
>>>>> R version 2.5.0 (2007-04-23)
>>>>> i686-redhat-linux-gnu
>>>>>
>>>>> locale:
>>>>>
>>>>>
>>>>> LC_CTYPE
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_NUMERIC
>>>>> =
>>>>> C
>>>>> ;LC_TIME
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_COLLATE
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_MONETARY
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_MESSAGES
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_PAPER
>>>>> =
>>>>> zh_CN
>>>>> .GB18030
>>>>> ;LC_NAME
>>>>> =
>>>>> C
>>>>> ;LC_ADDRESS
>>>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] "tools" "stats" "graphics" "grDevices" "utils"
>>>>> "datasets"
>>>>> [7] "methods" "base"
>>>>>
>>>>> other attached packages:
>>>>> cint06a520380fcdf affy affyio
>>>>> Biobase
>>>>> "1.14.0" "1.14.2" "1.4.1"
>>>>> "1.14.1
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>>
>>>>> --
>>>> Robert Gentleman, PhD
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M2-B876
>>>> PO Box 19024
>>>> Seattle, Washington 98109-1024
>>>> 206-667-7700
>>>> rgentlem at fhcrc.org
>>>>
>>>>
>>>
>>>
>>>
>> --
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>>
>
>
>
> --
> //-----------------------------------------------------------------------------------------
> // We have a hunger of the mind which asks for knowledge
> // of all around us, and the more we gain, the more is
> // our desire; the more we see, the more we are capable
> // of seeing.
> //----------------------------------------------------------------------------------------
>
> Yisong Zhen, Ph.D (Davidson Lab)
> Molecular & Cellular Biology
> Molecular Cardiovascular Research Program
> University of Arizona
> 1656 E. Mabel, MRB 317
> Tucson, AZ 85724 USA
> Lab: 520-626-8153
> Cell: 520-977-7397
>
> @---------------------------------------------------------------------------------------
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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