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")

(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?



(3) of the .qcdef file, what is the meaning of

0.05
0.065?



(4) I just want to find the outlier within one group of  4 chips, which
package should I use?

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@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@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@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@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@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@fhcrc.org
>>>
>>

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