[BioC] Quality control;Missing value;installation
Robert Gentleman
rgentlem at fhcrc.org
Tue Aug 12 21:07:59 CEST 2008
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Your R is very out of date, and we don't fix problems that are that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]]
>>>
>>> _______________________________________________
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>>>
>>>
>> --
>> 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
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