[BioC] library(affyQCReport)-NA(arg1); arrayQualityMetrics-no end
Robert Gentleman
rgentlem at fhcrc.org
Thu Aug 14 06:16:09 CEST 2008
Hi,
Yisong Zhen wrote:
> Dear all,
>
> I updated my R and Biocondcutor.
> I generated the cint06a520380fcdf.qcdef.
>
> (1)
> But when I use the library(affyQCReport), program still said that there had
> missing values (NA(arg1)).
>
> library(limma);
> library(affy);
> targets<-readTargets("targets.txt");
> data<-ReadAffy(filenames=targets$FileName);
>
> library(affyQCReport);
> setQCEnvironment("cint06a520380fcdf", "/home/Ry/TC_LC")
> QCReport(data, file="ExampleQC.pdf")
>
where is the output? Please provide complete examples, and always
include the output of sessionInfo(). I realize that you think you have
updated, but many of the problems of this sort are due to incorrect or
incomplete installations, so please always include the output of
sessionInfo().
Also, right after the error, you can call traceback to find out just
where the program failed. This will often help in any diagnosis.
> (2)
>
> When I used arrayQualityMetrics, it always took too long time. And I only
> got the MA1.pdf and foreground1.png. The program seemed to be no response. I
> had to interrpute it by CTRL+C. Why?
No idea, since you don't provide complete examples of inputs and
outputs and don't provide sessionInfo, we can't tell if it is a problem
with your setup or a bug that needs some other intervention.
You could try using debug and then step through the
arrayQualityMetrics function one line at a time. This will help to
determine where the problem is.
From the MA plot you can answer some of question 4 below.
>
>
>
> (3) of the .qcdef file, what is the meaning of
From where? Please try to provide more complete questions.
>
> 0.05
> 0.065?
>
>
>
> (4) I just want to find the outlier within one group of 4 chips, which
> package should I use?
I don't understand what you mean by this. What kind of outlier?
Most of the methods in arrayQualityMetrics and affyQCReport can be
called directly (eg some functions are in simpleaffy, some in affyPLM,
density or MA plots are easily constructed), so you should be able to do
all of them individually using the different packages. And if you got
the MA plot above, then that is one part of this.
Robert
>
> Thanks a lot. :)
>
>
>
> Yisong
>
>
>
>> 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
> limma_2.14.5
>
> loaded via a namespace (and not attached):
> [1] grid_2.7.1 KernSmooth_2.22-22
>
>
>
>
>
>
>
>
>
> On 8/12/08, Mark Cowley <m.cowley at garvan.org.au> wrote:
>> 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
>>>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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> 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
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